Transcriptome transfer produces cellular phenotype conversion

ABSTRACT

The present invention includes methods for effecting phenotype conversion in a cell by transfecting the cell with phenotype-converting nucleic acid. Expression of the nucleic acids results in a phenotype conversion in the transfected cell. Preferably the phenotype-converting nucleic acid is a transcriptome, and more preferably an mRNA transcriptome.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. application Ser. No.12/086,471, filed on Jun. 13, 2008, which is the National Stageapplication of PCT International Application No. PCT/US2006/047480,filed on Dec. 12, 2006, which in turn claims the benefit pursuant to 35U.S.C. § 119(e) of U.S. Provisional Application No. 60/749,941, filed onDec. 13, 2005; and also claims the benefit pursuant to 35 U.S.C. §119(e) of U.S. Provisional Application No. 61/167,286, filed on Apr. 7,2009, each of which is hereby incorporated by reference in its entiretyherein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was supported in part by funds obtained from the U.S.Government (National Institutes of Health Director's Pioneer Awardnumber DP1-OD-04117 and National Institutes of Health grant numberT32-MH14654), and the U.S. Government therefore has certain rights inthe invention.

BACKGROUND OF THE INVENTION

Cellular phenotype is the conglomerate of multiple cellular processesinvolving gene and protein expression that result in the elaboration ofa cell's particular morphology and function. It has been thought thatdifferentiated post-mitotic cells have their genomes hard wired withlittle ability for phenotypic plasticity. Emerging evidence has,however, demonstrated the reversibility and flexibility of the cellularphenotype. It has been shown that fertile adult male and female frogscan be obtained by injecting endoderm nuclei into enucleated eggs(Gurdon J B, Elsdale T R, & Fischberg M (1958) Sexually matureindividuals of Xenopus laevis from the transplantation of single somaticnuclei. Nature 182(4627):64-65). This result not only forms thefoundation of the field in nuclear transplantation, but also providesevidence that the cytoplasmic components of a differentiated cell cansupport nuclear reprogramming. Generation of induced pluripotent stem(iPS) cells by transfection transcription factors into dividingfibroblasts (Takahashi K & Yamanaka S (2006) Induction of pluripotentstem cells from mouse embryonic and adult fibroblast cultures by definedfactors. Cell 126(4):663-676), followed by cell selection represent anew strategy to globally revert a mature cell into a different celltype. See: Huangfu D, et al. (2008) Induction of pluripotent stem cellsfrom primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol26(11):1269-1275; Kim J B, et al. (2008) Pluripotent stem cells inducedfrom adult neural stem cells by reprogramming with two factors. Nature454(7204):646-650; Nakagawa M, et al. (2008) Generation of inducedpluripotent stem cells without Myc from mouse and human fibroblasts. NatBiotechnol 26(1):101-106; Maherali N, et al. (2007) Directlyreprogrammed fibroblasts show global epigenetic remodeling andwidespread tissue contribution. Cell Stem Cell 1(1):55-70; Okita K,Ichisaka T, & Yamanaka S (2007) Generation of germline-competent inducedpluripotent stem cells. Nature 448(7151):313-317; and Stadtfeld M,Nagaya M, Utikal J, Weir G, & Hochedlinger K (2008) Induced PluripotentStem Cells Generated Without Viral Integration. Science322(5903):945-949. The need for re-differentiation of these ES-like-iPScells into desired cell types, however, adds a layer of complexity thatis difficult to control (Wernig M, et al. (2008) Neurons derived fromreprogrammed fibroblasts functionally integrate into the fetal brain andimprove symptoms of rats with Parkinson's disease. Proc Natl Acad SciUSA 105(15):5856-5861; Hanna J, et al. (2007) Treatment of sickle cellanemia mouse model with iPS cells generated from autologous skin.Science 318(5858):1920-1923). Nevertheless, studies of nuclearreprogramming from genomic and epigenetic modification, as seen fromsomatic-cell-nuclear-transfer-cloned animals and iPS cells, suggests theflexibility of a differentiated phenotype as well as the dynamic changesof a genome (Maherali N, et al. (2007) Directly reprogrammed fibroblastsshow global epigenetic remodeling and widespread tissue contribution.Cell Stem Cell 1(1):55-70).

Despite the development and refinement of the techniques discussedabove, there remains a need in the art for methods and compositions foreffecting phenotypic change in a cell. This invention addresses thatneed.

BRIEF SUMMARY OF THE INVENTION

The present invention encompasses a method of effecting phenotypeconversion in a cell. The method comprises transfecting a second cell,the recipient cell, having a particular phenotype withphenotype-converting nucleic acid from a first cell, the donor cell,having a particular phenotype, wherein the phenotype of the first cellis different from that of the second cell. In some embodiments, thephenotype of the first cell differs from the phenotype of the secondcell by one or more of: species, tissue type, differentiation degree,disease state, exposure to a toxin, exposure to a pathogen, and exposureto a candidate therapeutic. Optionally, the method further comprisestransfecting the second cell at least a second time with the first cellmRNA transcriptome.

Preferably, the phenotype-converting nucleic acid is the transcriptomeand more preferably the mRNA transcriptome of the first cell. In oneembodiment, the the mRNA transcriptome comprises mRNA transcripts havingan average size between about 1 kb to about 5 kb.

In some embodiments, the phenotype-converting nucleic acid furthercomprises one or more exogenous nucleic acids selected from the groupconsisting of mRNA, siRNA, miRNA, hnRNA, tRNA, non-coding RNA andcombinations thereof.

In some embodiments, the transfecting step comprises irradiating thecell with a laser, wherein the cell is bathed in a fluid comprising thefirst cell mRNA transcriptome. Optionally, the irradiating step cancomprise 2 to 25 laser excitation pulses, wherein the laser is directedto different site on the second cell for each laser excitation pulse.

In some embodiments, the second cell is contacted with an exogenoustranscription inhibition agent prior to the transfecting step.Alternatively, in other embodiments, the second cell is notsubstantially contacted with an exogenous transcription inhibition agentbefore, during or after the transfecting step.

In some embodiments, the cell is selected from the group consisting of aeukaryotic cell and a prokaryotic cell. The eukaryotic cell can be anon-mammalian cell or it can be a mammalian cell. In some embodiments,the eukaryotic cell is a human cell.

In some embodiments, phenotype conversion comprises a change in one ormore of gene expression, protein expression, immunological markers,morphology, physiology, synthesis of bioproducts, and membrane lipidcomposition. In some embodiments, phenotype conversion comprises achange in expression of at least 100 genes. Phenotype conversion cancomprise up-regulation of genes associated with chromosomal remodeling.In some embodiments, at least about 5% of differentially expressed genesin the second cell change expression to a level observed for the firstcell.

In some embodiments, phenotype conversion persists for at least 2 weeks.In other embodiments, phenotype conversion persists for the lifetime ofthe cell.

In one embodiment, the second cell is a hair cell that responds to afirst range of sound frequencies. Optionally, the first cell is a haircell that responds to a second range of sound frequencies.

In another aspect, the invention provides a method of preparing a cellenriched for the presence of a second messenger system pathway. Themethod comprises the steps of transfecting a heterogenous collection ofmRNAs encoding the components of a second messenger system pathway intoa cell, wherein expression of the transfected heterogenous collection ofmRNAs enriches the presence of the second messenger system pathway.Optionally, the method further comprising transfecting the cell withsiRNA corresponding to one or more components of a different secondmessenger system pathway, thereby reducing expression of the componentsof the different second messenger system pathway.

In yet another aspect, the invention provides a method of deleting agene of interest in a cell. The method comprises transfecting an mRNAencoding an enzyme capable of sequence specific excision into a cell.The cell comprises chromosomal material that comprises a gene ofinterest flanked by recognition sequences specific for the enzymecapable of sequence specific excision. Expression of the mRNA providesthe enzyme capable of sequence specific excision. The enzyme then bindsto the enzyme recognition sequences and excises the gene of interest.The enzyme capable of sequence specific excision can be selected fromthe group consisting of CRE recombinase, FLP recombinase, zinc fingernuclease and combinations thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

For the purpose of illustrating the invention, there are depicted in thedrawings certain embodiments of the invention. However, the invention isnot limited to the precise arrangements and instrumentalities of theembodiments depicted in the drawings.

FIGS. 1A-1C depict a representative timeline for an embodiment of themethod of the invention, and graphs relating to characterization of arepresentative transcriptome. FIG. 1A depicts a representative timelineof sequential phototransfections. A first phototransfection (PT) wasperformed on hippocampal neurons, with local delivery of the astrocytetranscriptome. The same procedure was repeated 48 hrs and 7 days afterthe first phototransfection. Single cell mRNA harvesting,immunocytochemistry and physiological assessment were performed atvarious times subsequent to the third phototransfection. FIG. 1B is agraph of simulation data developed to estimate the efficacy of mRNAtransfer though a standard phototransfection pulse. Transport ofmolecules across the plasma membrane using phototransfection with laserirradiation can be controlled through both the number of pulses andextracellular nucleic acid concentrations in the method. FIG. 1C is ahistogram (dashed line) of the size distribution of the transcripts insolution during an exemplary phototransfection. The bars show the amountof the transcript delivered into the cytosol for a given transcriptsize.

FIGS. 2A and 2B depict schematics related to simulations of thephototransfection procedure. FIG. 2A depicts a schematic of laserexcitation pulses and resultant membrane permeability. FIG. 2B is aschematic depicting 16 separate regions (shaded ovals) of laserexcitation (250 nm in diameter). A distribution of membrane pore sizes(bottom schematic) is assumed to form in each region of laserexcitation. Although the exact pore size is not known, it is assumedthat the distribution of pore sizes were Gaussian, as depicted in thegraph on the bottom right.

FIGS. 3A to 3C are a series of a table, images and a graph related toexpression of astrocytic and neuronal mRNA and protein markers inneuronal cells transfected with astrocyte transcriptomes (N-TIPeR-AScells). FIG. 3A is a table summarizing single cell RT-PCR results.Single cell RT-PCR was performed on N-TIPeR-AS cells at different timepoints to detect the expression of GFAP and MAP2 genes. Age was definedas time post the third phototransfection. “+” indicates the presence ofGFAP or MAP2 mRNA. GFAP positive cells are highlighted in light gray. Apopulation of brain cortex cells containing both neurons and astrocyteswere used as positive control. Water was the negative control. FIG. 3Bis a series of images of a representative N-TIPeR-AS cell immunostainedfor all NeuN, GFAP and fibronectin antibodies two weeks post the thirdphototransfection. Scale bar=10 μm. FIG. 3C is a graph depicting resultsof immunocytochemistry studies of neurons, astrocytes and N-TIPeR-AScells. The graph shows that integrated immunofluorescence signal fromregions of interest. Immunoreactivity was tested for Dynamin 1 and GFAP.Astrocyte (triangle). Neuron (square). TIPeR cell (circle).

FIGS. 4A-4D are graphs and images depicting global gene expressionpatterns of TIPeR cells. FIG. 4A is a schematic depicting UPGMAclustering of the cell conditions on 3104 informative genes, with majorbranches labeled with bootstrap support indicating confidence in eachcluster. Leaves are colored different shades of gray according to celltype: charcoal=neurons (N); dark gray=N-TIPeR-N controls (C); lightgray=astrocyte (Astro)s; white=TIPeRed cells (TIPeR). FIG. 4B is a graphof the 3104-dimensional standard gene space reduced to three dimensionsof biological interest: 1st axis representing genes most variable forastrocyte vs neurons, 2^(nd) axis representing genes most variablebetween the TIPeR cells (i.e., representing TIPeR treatmentvariability), and the 3^(rd) axis representing overall variability ofall cells (astrocytes; neurons; control; neuro-TIPeR; astro-TIPeR, i.e.,the TIPeR cells clustering closest to the astrocytes as shown in thedendrogram in 4A). The transparent “cloud” around the points showsnon-parametric density contours. FIG. 4C is an image of a heatmapshowing intensity of 512 distinguishing probes across astrocytes(Astro), astro-TIPeRs (astro-TIPeR), N-TIPeR-N controls (Ctrl), andneurons (Neuro). Probes are separated by white lines into four groupsaccording to the intensities of the astro-TIPeR cells compared to theintensities of the neurons and the astrocytes: (I) astro-TIPeRexpression is similar to astrocytes but not neurons (201 probes); (II)astro-TIPeR expression is intermediate between astrocytes and neurons(77 probes); (III) astro-TIPeR expression is similar to neurons but notastrocytes (202 probes); (IV) astro-TIPeR expression is dissimilar toboth neurons and astrocytes (32 probes). Each lane is the data from anindividual cell. FIG. 4D is an image of a heatmap of 171 probes that aresignificantly quiescent in both astrocytes (Astro) and neurons (Neuro);followed in TIPeR cells 1 week (TIPeR 1w), 2 weeks (TIPeR 2w), and 4weeks (TIPeR 4w) post phototransfection; and for control cells (Ctrl).Each lane is the data from an individual cell.

FIGS. 5A-5C depict a table of genes activated after TIPeR. The tablelists the 65 probes (out of 171 probes) with significantly lowexpression levels in astrocytes and neurons that are significantlyup-regulated in N-TIPeR-AS cells. Gene annotations and p-value for eachgroup are listed. Significant (p<0.05) p-values are bolded.

FIG. 6 is a table of GO terms enriched in the N-TIPeR-AS. The tablelists the significant GO annotation terms enriched among 49 genesup-expressed in the N-TIPeR-AS cells 1-wk post the last transfection.Aspect abbreviations: MF=molecular function, CC=cellular component,BP=biological process.

FIGS. 7A-7D depict a table of data related to GO enrichment analysis.Analysis was on sets of probes distinguishing different cell conditions:GO aspect (Biological Process, Cellular Component, Molecular Function),term, and enrichment p-value for significantly enriched GO annotationterms among each subset of genes showing differential expression amongthe different cell conditions, as labeled.

FIG. 8A-8C is a series of images and graphs depicting morphologicalanalysis of TIPeR cells. FIG. 8A is a series of DIC images of arepresentative N-TIPeR-N cell (left panel) and an representativeN-TIPeR-AS cell (right panel). Scale bar=20 FIG. 8B is a bar graph orrelative cell size of N-TIPeR-N cells cultured in the neuronal medium(NB), N-TIPeR-N cells and N-TIPeR-AS cells. The Y-axis is the percentageof change in overall cell size when comparing that of post-TIPeR to theinitial cell size. Error bars represent the value of standard error ofthe mean (SEM). FIG. 8C is a bar graph regarding process retraction forN-TIPeR-N cells cultured in the neuronal medium (NB), N-TIPeR-N cellsand N-TIPeR-AS cells. Process retraction occurs for N-TIPeR-As cellswith 65% of N-TIPeR-AS cells showing retraction of their processes whileonly 40% of N-TIPeR-N cells cultured in the astrocyte medium and 20% ofN-TIPeR-N cells cultured in the neuronal medium retracted theirprocesses. The dark gray bars correspond to % cells retaining neuronalprocesses. The black bars correspond to % cells that have lost neuronalprocesses.

FIG. 9 is a graph of percentage of N-TIPeR-AS cells displaying variousphysiological calcium fluctuation patterns as a function of time postthird phototransfection. “Astrocyte-like” refers to at least 5% increasein Fluo-4 intensity only upon glutamate (500 μM) but not KCl (50 mM)application in calcium fluctuation pattern. “Neuron-like” refers to atleast at least 5% increase in Fluo-4AM intensity upon both glutamate andKCl application in calcium fluctuation patter. “Non-specified”N-TIPeR-AS cells are the cells that show no detectable change uponglutamate application. Error bars are the SEM.

FIG. 10 is a series of three images of a representative TIPeRed cellthat was immunostained for MyoD (left image) and Connexin43 (middleimage). The right image combines the fluorescence for both the MyoD andConnexin43, with DAPI staining. The broad white arrows point to thenucleus of the cell. The narrow white arrows point to representativeDAPI-stained DNA. The cell is a mouse embryonic fibroblast that wastransfected twice with mouse cardiomyocyte mRNA, which was thenimmunostained two weeks after the first transfection.

FIG. 11 is a graph and a series of images depicting representativelevels of CBP immunoreactivity in mouse cells transfected with mRNAencoding CRE-recombinase and non-transfected mouse cells. The mousecells were obtained from a mouse genetically engineered to have the genefor CBP300 flanked by Lox P sites. The X axis is transfected ornon-transfected cells. Cells were transfected with two differentquantities of mRNA; the data on the far left is for cells transfectedwith 10-fold more mRNA than the data depicted in the middle of thegraph. The Y axis is the fluorescence intensity of CPB staining, whichis a reflection of the amount of CBP protein present in a cell. The datadepicted was obtained 7 days after transfection.

DETAILED DESCRIPTION OF THE INVENTION

cDNA microarray analysis has shown that phenotypic differences at thecellular level are associated with differences in the presence, absenceand abundances of particular RNAs. The invention described herein arisesfrom the discovery that the relative abundances of RNAs within apopulation themselves can elaborate cellular phenotype. Specifically,the invention provides a method of effecting a phenotype conversion inrecipient cell by introducing phenotype-converting nucleic acid from adonor cell into the recipient cell. In a preferred embodiment, thephenotype-converting nucleic acid is the mRNA transcriptome of the donorcell. The discovery described herein indicates that the plasticity ofthe non-dividing genome is much greater than previously imagined.

Phenotype-converting nucleic acid may include, without limitation, mRNA,siRNA, microRNA, tRNA, hnRNA, total RNA, DNA, and combinations thereof,such that the introduction of these nucleic acids into a cell and thesubsequent expression of these nucleic acids results in a combinedphenotype due to the multiple expression of these nucleic acids andtheir interactions with each other. Unlike expression systems known inthe art, where one or only a few nucleic acids are expressed, themethods of the present invention permit the expression of multiplenucleic acids essentially simultaneously, resulting in an expressionsystem closely mirroring the interaction of various nucleic acids andtheir expression products in a natural environment. Thus, the presentinvention permits the introduction of a complex mixture of nucleic acidsinto a cell to produce a multigenic effect, thereby effecting phenotypeconversion of a cell.

The methods of the present invention are performed by transfecting amixture of nucleic acids into live cells. In a preferred embodiment, thepresent invention includes methods for phenotype conversion of a cellusing laser-aided poration of live cell membranes coupled with bathapplication of nucleic acids, preferably a transcriptome, in order totransfect a mixture of nucleic acids into a live cell. Photoporation isadvantageous in enabling highly location-specific transfection of a celland permitting multiple poration events, while not detrimental tocellular function or viability.

The present invention permits the transfection of nucleic acid,preferably mRNA and/or DNA into a cell with accurate control of theamount of nucleic acid entering the cell, thus allowing the skilledartisan to mimic the expression level of nucleic acid in a cell underdesired conditions, as disclosed elsewhere herein. That is, the presentinvention allows the skilled artisan to accurately control the level ofnucleic acid transfected into a cell by modulating the concentration ofnucleic acid in the extracellular environment of the cell. Further, theprecise amount of nucleic acid transfected into a cell can be modulatedthrough regulation of laser intensity, pore size and number, andduration of membrane opening, as well as repetition of transfection.

The methods of the present invention are not limited to cells, but canfurther include live slices of tissue and live animals, preferablymammals, as disclosed elsewhere herein. The methods of the presentinvention can further comprise other non-mammalian cells eukaryoticcells and prokaryotic cells, such as bacterial cells, yeast cells, plantcells, protozoa, insect cells, fungal cells, including filamentous andnon-filamentous fungi, and the like.

Definitions

As used herein, each of the following terms has the meaning associatedwith it in this section.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e., to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

As used herein, “phenotype conversion” refers to the induction orestablishment of a destination phenotype. Phenotype conversion comprisesa change in at least one of gene expression, protein expression,immunological markers, morphology, physiology, synthesis of bioproducts(e.g., dopamine) and membrane lipid composition.

As used herein, a “destination phenotype” refers to a phenotype ofinterest that is induced in a recipient cell by the introduction thereinof a mixture of nucleic acids. The phenotype of interest may be anyphenotype. For example, a destination phenotype may be a morphologicalchange, such as the retraction of neuronal processes in a recipient cellthat is a neuron. A destination phenotype may be a physiological change,such as the presence of voltage-gated calcium receptors in a recipientcell that is an astroglial cell. A destination phenotype may comprisemore than one phenotypic change and may even cause the cell to assumecharacteristics of a different tissue type from its original tissuetype.

The phrase “phenotype-converting nucleic acid” refers herein to amixture of nucleic acid that is capable of establishing a destinationphenotype in a recipient cell. Phenotype-converting nucleic acid is notlimited to the empirical content of RNA in a donor cell, but rather,encompasses the relative abundance of each RNA with respect to each in apopulation of RNAs such that the population of RNAs are necessary andsufficient to induce a destination phenotype in a recipient cell.

As used herein, “transcriptome” refers to the collection of all genetranscripts in a given cell and comprises both coding RNA (mRNAs) andnon-coding RNAs (e.g., siRNA, miRNA, hnRNA, tRNA, etc). As used herein,an “mRNA transcriptome” refers to the population of all mRNA moleculespresent (in the appropriate relative abundances) in a given cell. AnmRNA transcriptome comprises the transcripts that encode the proteinsnecessary to generate and maintain the phenotype of the cell. As usedherein, an mRNA transcriptome may or may not further comprise mRNAmolecules that encode proteins for general cell existence, e.g.,housekeeping genes and the like.

As used herein, “TIPeR” refers to the process of transfecting arecipient cell with a transcriptome from a donor cell. A cell that hasundergone this process may be referred to herein as a TIPeRed cell.

A “disease” is a state of health of an animal wherein the animal cannotmaintain homeostasis, and wherein if the disease is not ameliorated,then the animal's health continues to deteriorate. In contrast, a“disorder” in an animal is a state of health in which the animal is ableto maintain homeostasis, but in which the animal's state of health isless favorable than it would be in the absence of the disorder. Leftuntreated, a disorder does not necessarily cause a further decrease inthe animal's state of health.

A “fluid medium” or “fluid media” is used herein to refer to a form ofmatter, such as air, liquid, solid or plasma, preferably liquid, that iscapable of flowing.

An “isolated cell” refers to a cell which has been separated from othercomponents and/or cells which naturally accompany the isolated cell in atissue or mammal.

As applied to a protein, a “fragment” of a polypeptide, protein or anantigen, is about 6 amino acids in length. More preferably, the fragmentof a protein is about 8 amino acids, even more preferably, at leastabout 10, yet more preferably, at least about 15, even more preferably,at least about 20, yet more preferably, at least about 30, even morepreferably, about 40, and more preferably, at least about 50, morepreferably, at least about 60, yet more preferably, at least about 70,even more preferably, at least about 80, and more preferably, at leastabout 100 amino acids in length amino acids in length, and any and allintegers there between.

A “genomic DNA” is a DNA strand which has a nucleotide sequencehomologous with a gene as it exists in the natural host. By way ofexample, a fragment of a chromosome is a genomic DNA.

As used herein, an “inhibitory nucleic acid” refers to an siRNA, amicroRNA, an antisense nucleic acid or a ribozyme.

As used herein, “locally transfecting” a nucleic acid refers tointroducing a nucleic acid into a region of cytoplasm that is not theentirety of the cytoplasm of a cell optionally comprising a cellularprocess.

As used herein, “porate” or “porates” refers to creating a hole in asurface through which compounds can pass.

“Homologous” as used herein, refers to the subunit sequence similaritybetween two polymeric molecules, e.g., between two nucleic acidmolecules, e.g., two DNA molecules or two RNA molecules, or between twopolypeptide molecules. When a subunit position in both of the twomolecules is occupied by the same monomeric subunit, e.g., if a positionin each of two DNA molecules is occupied by adenine, then they arecompletely or 100% homologous at that position. The percent homologybetween two sequences is a direct function of the number of matching orhomologous positions, e.g., if half (e.g., five positions in a polymerten subunits in length) of the positions in two compound sequences arehomologous then the two sequences are 50% identical, if 90% of thepositions, e.g., 9 of 10, are matched or homologous, the two sequencesshare 90% homology. By way of example, the DNA sequences 5′ATTGCC3′ and5′ TATGGC3′ share 50% homology.

In addition, when the terms “homology” or “identity” are used herein torefer to the nucleic acids and proteins, it should be construed to beapplied to homology or identity at both the nucleic acid and the aminoacid sequence levels.

The term “multigenic phenotype” is used herein to refer to a phenotypein a cell, tissue or animal that is mediated by the expression or lackof expression of two or more nucleic acids encoding a protein, whereinthe nucleic acids are exogenously provided to the cell, tissue oranimal.

“Recombinant polynucleotide” refers to a polynucleotide having sequencesthat are not naturally joined together. An amplified or assembledrecombinant polynucleotide may be included in a suitable vector, and thevector can be used to transform a suitable host cell.

A recombinant polynucleotide may serve a non-coding function (e.g.,promoter, origin of replication, ribosome-binding site, etc.) as well.

A host cell that comprises a recombinant polynucleotide is referred toas a “recombinant host cell.” A gene which is expressed in a recombinanthost cell wherein the gene comprises a recombinant polynucleotide,produces a “recombinant polypeptide.”

A “recombinant polypeptide” is one which is produced upon expression ofa recombinant polynucleotide.

“Polypeptide” refers to a polymer composed of amino acid residues,related naturally occurring structural variants, and syntheticnon-naturally occurring analogs thereof linked via peptide bonds,related naturally occurring structural variants, and syntheticnon-naturally occurring analogs thereof. Synthetic polypeptides can besynthesized, for example, using an automated polypeptide synthesizer.

The term “protein” typically refers to large polypeptides.

The term “peptide” typically refers to short polypeptides.

Conventional notation is used herein to portray polypeptide sequences:the left-hand end of a polypeptide sequence is the amino-terminus; theright-hand end of a polypeptide sequence is the carboxyl-terminus.

“Phototransfection” is used herein to refer to a process by which a holeis created in a barrier, such as a cell membrane, using a photon source,such as a laser, and two or more nucleic acids, wherein the nucleicacids encode different polypeptides, are inserted into a cell throughthe hole in the cell membrane.

By “tag” polypeptide is meant any protein which, when linked by apeptide bond to a protein of interest, may be used to localize theprotein, to purify it from a cell extract, to immobilize it for use inbinding assays, or to otherwise study its biological properties and/orfunction.

It is understood that any and all whole or partial integers between anyranges set forth herein are included herein.

DESCRIPTION

The present invention provides methods of introducing mixtures ofnucleic acids into a recipient cell to produce a phenotype-conversion inthe recipient cell. The present invention comprises transfectingphenotype-converting nucleic acid, preferably RNA and/or DNA, even morepreferably mRNA, and most preferably, an mRNA transcriptome, locallyinto a recipient cell. The phenotype of the donor cell is different fromthe phenotype of the recipient cell. The difference in phenotype may beany difference, such a difference in species, tissue type, extent ofdifferentiation, exposure to a drug or pathogen, disease state, growthconditions and so forth, wherein the difference is known or suspected ofresulting from a difference in gene expression.

As shown herein, transfection with an mRNA transcriptome yields a highdegree of phenotype conversion. Where multiple cells are transfected inaccordance with the method of the invention, at least about 25% of thecells undergo phenotype conversion. In some embodiments, phenotypeconversion in at least about 35% of recipient cells is observed.

The recipient cell may be any type of cell. A recipient cell may be aneukaryotic cell or a prokaryotic cell. When the cell is an eukaryoticcell, the cell is preferably a mammalian cell, including but not limitedto human, non-human primate, mouse, rabbit, rat, goat, guinea pig, horsecell, and the like. A non-mammalian eukaryotic cell includes a yeastcell, a plant cell, an insect cell, a protozoan cell and a fungal cell,including filamentous and non-filamentous fungi. When the cell is aprokaryotic cell, the cell is a bacterial cell. A recipient cell may bea differentiated cell and/or a non-dividing cell. The cell may also be aprogenitor cell or a stem cell. Preferably, the recipient cell is atissue-specific cell, more preferably a mammalian tissue-specific celland more preferably still, a human tissue-specific cell. Non-limitingexamples of cells suitable as recipient cells include epithelial cells,neurons, fibroblasts, embryonic fibroblasts, keratinocytes, adult stemcells, embryonic stem cells, and cardiomyocytes.

To obtain the desired phenotype conversion, recipient cells arepreferably phenotypically-pliable cells. Phenotypically-pliable cellsare cells whose phenotype is amenable to changing under the conditionsof the method of the invention. Non-limiting examples ofphenotypically-pliable cells include neurons, fibroblasts, embryonicfibroblasts, adult stem cells and embryonic stem cells. Preferably, thecell is a neuron, and comprises a cellular process such as a dendrite,and the nucleic acid is RNA, even more preferably, mRNA and morepreferably still, an mRNA transcriptome.

In the method of the invention, nucleic acid is transferred into a cellto initiate phenotype conversion in the recipient cell. As used herein,phenotype conversion comprises a change in at least one of geneexpression, protein expression, immunological markers, morphology,physiology, synthesis of bioproducts (e.g., dopamine) and membrane lipidcomposition. Preferably, the change yields a phenotype associated withor indicative of the cell from which the transfected RNA or DNA isobtained. Preferably, phenotype conversion in the recipient cellcomprises two or more changes. More preferably, phenotype conversioncomprises three or more changes. In one embodiment, phenotype conversioncomprises a change in physiology. In another embodiment, phenotypeconversion comprises a change in morphology and a change in physiologyof the recipient cell. As shown herein, phenotype conversion may beaccompanied by changes in expression in hundreds of genes. For instance,expression of genes quiesent in both the donor and the recipient cellsmay be de novo up-regulated. Genes associated with chromosomalremodeling, such as genes involved in chromosome and DNA metabolismrelated process, may be up-regulated in cells having phenotypeconversion. See “BP” terms in FIGS. 6 and 7. Genes annotated “BP” in theGene Ontology (“GO”) database are considered associated with chromosomalremodeling (The Gene Ontology Consortium (2000) “Gene ontology: tool forthe unification of biology,” Nature Genet. 25:25-29). The GO database ispublicly available (see www(dot)geneontology(dot)org). In someembodiments, at least about 5%, more preferably about 7%, 10%, 15% andmore preferably still at least about 25% of genes that are expresseddifferently in the recipient cell compared to the donor cell (e.g.,differentially expressed genes) based on gene expression profiling havetheir expression changed to the level observed for the donor cell.

Phenotype conversion in the recipient cell is maintained stably forextended periods of time. In one embodiment, phenotype conversion isstable and persists for at least about 1 day, 2 days, 3 days, 4 days, 5days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13days, or more. In one embodiment, phenotype conversion is stable for atleast about 1 week, 2 weeks, 3 weeks, 4 weeks, or more. In anotherembodiment, phenotype conversion is stable for at least about 1 month, 2month, 3 months or more. In preferred embodiments, phenotype conversionis stable for the duration of the recipient cell's lifespan or thelifespan of a culture derived from the recipient cell.

Phenotype-converting nucleic acid may comprise two or more nucleic acidshaving different sequences. In some embodiments, the two or more nucleicacids encode different polypeptides. In other embodiments, the nucleicacids are non-coding RNAs or other non-coding nucleic acids. In yetother embodiments, the nucleic acids comprise a mixture of coding andnon-coding nucleic acids. In preferred embodiments, thephenotype-converting nucleic acid comprises the transcriptome,preferably the mRNA transcriptome, from a donor cell. In otherembodiments, the phenotype-converting nucleic consists only of thetranscriptome or mRNA transcriptome from a donor cell. Nucleic acids maybe obtained from a donor cell or may be chemically synthesized or acombination thereof. Methods for chemically synthesizing a nucleic acidare disclosed elsewhere herein and can include in vitro transcription.

An mRNA transcriptome may comprise mRNAs encoding 3 or more, 5 or more,10 or more, 20 or more, 40 or more, 50 or more, 75 or more, 100 or more,200 or more different polypeptides.

The method of the invention may be carried on a cell comprising acellular process. Such a cellular process includes, but is not limitedto, a dendrite, an axon, a microvilli, a cilia, a stereocilia, aprocess, an astrocytic process, and the like. As demonstrated herein,this method advantageously permits the introduction of a desired amountof nucleic acid into one or more local sites, permitting the controlledand localized production of protein in physiological amounts, resultingin a multigenic effect in a cell. This method thus allows specificlocalization of exogenously applied nucleic acid, preferably mRNA,without resorting to severing the cellular process from the cell towhich it is attached (Kacharmina, et al., 2000, Proc. Nat'l Acad. Sci.USA, 97:11545-11550). Further, the present method permits the expressionof an mRNA transcriptome of a donor cell, thus resulting in phenotypeconversion in the recipient cell.

The present invention further comprises methods for phototransfecting alive slice of tissue or a live animal. Methods for sustaining thecellular processes in the cells comprising a live slice of tissue areknown in the art. As a non-limiting example, live slices can berefrigerated and perfused with natural or artificial fluids, such asartificial spinal fluid, artificial central nervous system fluid, andbuffers disclosed elsewhere herein. Methods for the manipulation of liveslice cultures are described in, for example, Roelandse, et al. (2004,J. Neuroscience, 24: 7843-7847); and Chen, et al. (2005, Magn. Reson.Med. 53: 69-75).

Methods for phototransfecting a live animal, preferably a mammal, areperformed using the methods described herein combined with methods ofanimal and human surgery known in the art. Exemplary surgical procedurescontemplated for use with the methods of the invention include cardiaccatherization, angioplasty, arthroscopy, laproscopy, tumor resection,surgical placement of a therapeutic implant and the like. Mammalscontemplated in the present invention include, but are not limited to,mice, rabbits, rats, goats, guinea pigs, humans, and the like.

As a non-limiting example, a laser is applied to a tissue in a liveanimal to phototransfect the tissue in the live animal with one or morenucleic acids. The nucleic acid is introduced to the animal usingmethods disclosed elsewhere herein, such as through a microscope or anoptical fiber or endoscopy. The expression of a polypeptidephototransfected using the methods of the present invention is monitoredusing methods of detecting protein expression known in the art, such asWestern blots, immunocytochemistry, in situ protein detection, and thelike. Methods for using a laser to manipulate animal tissues are wellknown in the art and are described in, for example, Dang, et al. (2005,Exp Dermatol., 14: 876-882).

The methods disclosed herein comprise introducing phenotype-convertingnucleic acid, preferably RNA and more preferably mRNA, siRNA, miRNA,hnRNA, tRNA, non-coding RNAs and combinations thereof, including but notlimited to total mRNA, to a cell that optionally comprises a cellularprocess, preferably a neuron comprising a dendrite, andphototransfecting the cell at one or more sites on the cell membrane.Preferably, the phenotype-converting nucleic acid introduced into a celloptionally comprising a cellular process is an mRNA transcriptome. Thecell is preferably a primary cell culture or in slice culture. The celloptionally comprising a cellular process can be phototransfected at anysite. Preferably, the site is on a cellular process, such as a dendrite,or the cell body, such as the soma. The nucleic acid can be provided tothe cell comprising a cellular process by any method known to theskilled artisan, and is preferably provided by means of a nucleic acidbath comprising a mixture of nucleic acids, disclosed elsewhere herein.A nucleic acid bath is a solution comprising a nucleic acid of interestin which a cell is bathed. In one embodiment, bath application of thecell comprises surrounding the cell with a solution comprising nucleicacid, thus bathing the entire cell. The cell is then irradiated with alaser at one or more sites located anywhere on the cell. In anotherembodiment, bath application comprises bathing a discrete portion orportions of a live cell, for instance, by applying a solution comprisingnucleic acid to a discrete location on the surface of the cell. The cellis then irradiated one or more times within the discrete location orlocations that was bathed. The discrete location bath is advantageousbecause it creates a greater mRNA concentration gradient, which allowsmRNAs to diffuse more efficiently through the temporary poration holesinto the porated cell. It also requires less mRNAs (e.g., 0.3 μg) thanthe bath application (e.g., 20 μg). In either case, the solution isappropriately buffered and is of the proper pH to maintain thestructural integrity of the cell to be phototransfected.

Phenotype-converting nucleic acid suitable for use in the method of theinvention may be of any size. For instance, a nucleic acid of about 800nucleotides and a nucleic acid of about 3000 nucleotides have beensuccessfully phototransfected into cells comprising a cellular processusing the inventive procedure. However, the methods of the presentinvention are not limited to a nucleic acid, preferably an RNA, of thesizes disclosed herein. The present invention comprisesphototransfecting a nucleic acid of about 30 bases, even morepreferably, about 50 bases, yet more preferably, about 75 bases, evenmore preferably, about 100 bases, yet more preferably, about 75 bases,even more preferably, about 100 bases, yet more preferably, about 150bases, even more preferably, about 200 bases, yet more preferably, about300 bases, even more preferably, about 500 bases, yet more preferably,about 750 bases, even more preferably, about 1000 bases, yet morepreferably, about 1500 bases, even more preferably, about 2000 bases,yet more preferably, about 2500 bases, even more preferably, about 3000bases, in length. Even more preferably, the present invention comprisestransfecting, preferably by phototransfection, a mixture of RNAsencoding different proteins and of different molecular weights. Inpreferred embodiments, the phenotype-type converting nucleic acid is anmRNA transcriptome having a range of mRNA transcript sizes and having anaverage mRNA transcript size from about 0.5 kb to about 5 kb, morepreferably, from about 1 kb to about 3.5 kb. As a non-limiting example,the mRNA transcriptome is obtained from an astrocyte, wherein theaverage size of the mRNA transcriptome is about 1.5 kb. Thetranscriptome is transfected into a recipient cell, such as a neuron, toinduce phenotype conversion of the neuron to the astrocyte phenotype.

As another non-limiting example, a nucleic acid expression profile of acell in a desired physiological state (e.g. during differentiation, in adisease state, after treatment with a pharmaceutical, toxin or othercompound) and a nucleic acid expression profile of a cell in anotherphysiological state (e.g. the same cell type pre- orpost-differentiation, not in a disease state, or before treatment with apharmaceutical, toxin or other compound) can be obtained usingtechniques for RNA isolation known in the art and disclosed elsewhereherein. The cDNA clones of these RNAs can be generated, reflecting thealtered RNA abundances of the differing physiological states, or the RNAcan be transfected into a cell without first reverse transcribing theRNA to cDNA. These RNA can be mixed according to the same ratios andabundances indicated by the nucleic acid expression profiles of thecells in differing physiological states. These nucleic acid mixtures arethen transfected into a cell using the phototransfection methodsdisclosed herein. The methods of the present invention permit the localtransfection of a cell, and therefore the nucleic acid mixture can belocally transfected to a specific part of a cell, such as the soma, anastrocytic process, a dendrite, or another cellular process, or thenucleic acid mixture can be generally transfected into a cell byphototransfecting any portion of the cell. Using the methods of thepresent invention, and the physiologically relevant mixtures of nucleicacids described herein, once the mixture of nucleic acids is expressedin a cell, the phenotype of the physiological state can be replicated ina cell or a cellular process, thus allowing the skilled artisan toobserve the phenotype transfer in a cell or cellular process.

Nucleic acid, preferably a transcriptome, may be obtained from any cellof interest in any physiological state. The donor cell may be any typeof cell. A donor cell may be an eukaryotic cell or a prokaryotic cell.When the cell is an eukaryotic cell, the cell is preferably a mammaliancell, including but not limited to human, non-human primate, mouse,rabbit, rat, goat, guinea pig, horse cell, and the like. A non-mammalianeukaryotic cell includes a yeast cell, a plant cell, an insect cell, aprotozoan cell and a fungal cell, including filamentous andnon-filamentous fungi. When the cell is a prokaryotic cell the cell is abacterial cell. Non-limiting examples of cells from which nucleic acidmay be obtained include astrocytes, cardiomyocytes, neonatalcardiomyocytes, embryonic stem cells and neurons. RNA from any donorcell of interest can be phototransfected into any recipient cell in themethod of the invention. Preferably, donor cells are of the same speciesas the recipient cells. Donor cells may be from the same individual asthe recipient cell, or from a different individual. Donor cells mayoriginate from the same germinal layer (e.g., ectoderm) as the recipientcell (e.g. both arise from ectoderm germ layer), or from a differentgerminal layer (e.g., one cell arises from ectoderm and the other arisesfrom endoderm germ layer). Donor cells may be the same cell type as therecipient cell but at a different stage of differentiation, exposed to acandidate therapeutic, exposed to a toxin or pathogen, diseased. In yetother embodiments, a donor cell may be a recipient cell. For instance,nucleic acid from a donor cell is transferred into a first recipientcell. Nucleic acid from the first recipient cell is then subsequentlytransferred into a second recipient cell. In one aspect, the first andsecond recipient cells are in different physiological states. In anotheraspect, the first and second recipient cells are the same type of cell.As described elsewhere herein, RNA obtained from a cell may be used totransfect a cell, or may be used as a template to create cDNA. The cDNAmay be used in in vitro transcription methods to amplify some or all ofthe RNA, which is then used in the method of the invention.

As a non-limiting example, the total RNA from a neuronal stem cell orother progenitor neuronal cell can be isolated from such a cell usingtechniques known in the art and disclosed elsewhere herein. To obtain anmRNA transcriptome, the total RNA can then be processed using variousmethods known in the art for isolating mRNA, such as isolation of mRNAusing complementary poly-dT nucleic acids, which can be conjugated tobeads or a column. The total mRNA obtained is then transfected into arecipient cell using the methods disclosed herein. The recipient cellthen expresses the mixture of mRNA isolated from the neuronal stem celland replicates the multigenic effect of the differential genetranslation and regulation characteristic of a developing neuronal stemcell. The present invention is not limited to neuronal stem cellshowever, and can be used to determine the transferred multigenicphenotype of any type of developing or developed cell, provided that thetotal RNA and mRNA are isolated from the cell.

In one embodiment, total RNA or the mRNA transcriptome isolated fromhair cells that respond to a particular frequency range (donor cells)can be isolated and transfected into a hair cell that responds to adifferent frequency range (recipient cells). In one aspect, the donorcell is a hair cell that responds to high frequencies. Exemplary highfrequencies include about 15,000-20,000 Hz. Phenotypic responsiveness inthe transfected cells can be assessed using morphological measurements(different frequency responders have different shapes) and/orphysiological responsiveness such as electrophysiologic measurements andCa′ influx. One of the major causes of age-related hearing loss is theloss of frequency responsive hair cells in the cochlea of the ear. Thus,this embodiment is contemplated to provide cells useful in the treatmentfor age-related hearing loss. Practice of this embodiment in vivo isfurther contemplated as treatment for age-related hearing loss.

As an alternative non-limiting example, the total RNA from a celltreated with a compound, such as a drug, a peptide, a cytokine, anantibody, a mitogen, a toxin, or other compounds known in the art, canbe isolated using the methods disclosed herein and known in the art. ThemRNA from that cell can then be transfected into another cell type usingthe methods disclosed herein, thus transferring the multigenic phenotypeof the cell treated with a compound to another cell, thus enabling therapid and specific determination of that compound on another cell type.

In another non-limiting embodiment of the present invention, the totalRNA from a diseased cell, such as a tumor cell, a cell harboring anintracellular pathogen, a cell from a patient with an autoimmunedisease, and the like, can be isolated from the diseased cell. The mRNAtranscriptome from that cell can be isolated from the total RNA using,for example, poly-dT isolation techniques. The mRNA from the diseasedcell is transfected into another cell using the methods of the presentinvention, thus transferring the multigenic phenotype of the diseasedcell to another cell, providing a more accurate picture of the roleinteracting nucleic acids and their encoded proteins have in thephenotype of a cell.

As another non-limiting embodiment of the invention, the method of theinvention can be practiced in order to prepare cells for testingtherapeutics. Candidate therapeutics are typically tested on a number ofdifferent cell types, prior to assessment in animals or humans. Thesedifferent cells often are cell lines that have a multiplicity ofsignaling pathways. The multiplicity of pathways may overlap andcompensate for drug function and testing with regard to efficacy and/orside effects, thereby making assessment of the candidate drug effectsless robust. According, it is contemplated that mRNA for one or morespecified second messenger system pathways can be transfected intoprimary cells or cell lines of interest in order to create cells havingenriched presence and/or activity of one or more pathways, thus thesepathways will dominate over endogenous pathways. The mRNA are thereforea heterogenous collection of mRNAs that encode the various componentsfor the one or more second messenger system pathways. Enriched presenceand/or activity of one or more pathways is relative to a cell that hasnot had mRNA for one or more specified second messenger system pathwaystransfected into it. Candidate therapeutics can then be assessed forefficacy and/or side effects on the dominant pathways present in thecells with enriched expression of one or more specified second messengersystem pathways. Non-limiting examples of second messenger systemsinclude: the cAMP system; the phosphoinositol system; the arachidonicacid system; the cGMP system; and the tyrosine kinase system. It isexpected that using such defined cell types permits improved assessmentof the effect of a candidate on particular pathways. In one embodiment,modulation of endogenous pathways by decreasing expression of particularpathways is also contemplated. Modulation can be achieved by introducingsiRNAs corresponding to mRNAs encoding particular proteins in a pathwayinto the cell to inhibit particular pathways. Such modulation can beperformed simultaneously with the introduction of the mRNAs for the oneor more specified second messenger system pathways, or can be done inone or more separate steps. In one embodiment, an embryonic fibroblastis used as the recipient cell. In one embodiment, the donor cells fromwhich total RNA is obtained are cardiomyocytes and the recipient celltype is an embryonic fibroblast. In a preferred aspect, mRNA isextracted from the cardiomyocyte total RNA and is transfected into theembryonic fibroblast.

In another non-limiting embodiment, the method of the invention can beused to generate a knock out (KO) of one or more specific genes in acell. The field of functional genomics has relied upon the generation ofKO mice to elucidate the function of particular genes. The utility of KOmice has been enhanced by flanking a gene with FLOX-sites, which arerecognized by CRE-recombinase. CRE-recombinase binds to FLOX-sites andremoves the intervening sequence containing the gene, thereby knockingout that gene. Cell-type specific KO has been achieved by drivingCRE-recombinase expression in particular cell types using cell-typespecific promoters. Inducible promoters, such as TET-on or the ecdysonesystem, have been used to control the time of induction ofCRE-recombinase expression; expression is induced upon exogenousaddition of the cognate inducer. Advantageously, the method of theinvention can be used to knock out a gene in a particular cell at aparticular time without the use of inducible promoters and exogenousinducers. In one embodiment, mRNA encoding CRE-recombinase, or theprotein itself, is transfected into cells having chromosomal materialengineered genetically to contain FLOX sites flanking one or more genesof interest. The transfection can be done with a single engineered cellor with a population of the engineered cells. The method can also bepracticed with live tissue samples or with a live animal. The method isnot limited to the use of CRE-recombinase and FLOX sites. It can bepracticed using any comparable system of specific sequence excision,such as zinc-finger nuclease technology and the FLP recombinase and FRTsystem. The method can also be used for targeted integration of a gene.

The present invention can further comprise the use of a nucleic acidfrom a cell or a population of cells of homogeneous or heterogeneoustypes. The present invention can further comprise the use of a nucleicacid, preferably mRNA, defined by the expression profile of a cell asdetermined using methods well known in the art, including, but notlimited to, a gene array profile, total RNA, total mRNA, and the like.An expression profile is used to determine the relative abundances ofmRNA in a cell. The expression profile is then used as a template todetermine the relative abundances of mRNA in the physiological state ofthe cell from which the expression profile was made. A population ofmRNA with the same relative abundance as in the cell for whichexpression has been profiled is produced using the methods disclosedelsewhere herein, including mRNA isolation, in vitro transcription orchemical synthesis. The resultant population of mRNA is thenphototransfected into the cell using the methods described elsewhereherein, thereby transferring the phenotype of the cell from which theexpression profile was made to another cell, tissue or animal.

In another embodiment, a population of mRNA reflecting the relativeabundance of a cell in a particular physiological state furthercomprises mRNA encoding one or more polypeptides that facilitatephenotype conversion. For instance, the mRNA obtained from a neuronalcell may be supplemented with mRNA encoding proteins that stimulateexocytosis and is then phototransfected into a non-neuronal recipientcell.

The present invention may further comprises the sequential transfection,preferably sequential phototransfection, of a cell. Sequentialtransfection is used herein to refer to a process in which a cell istransfected at a first time point, and then transfected at a second orsubsequent time point. As an example, a cell can be phototransfected onday 1, the result of which is that one or more nucleic acids areintroduced into the cell. These nucleic acids can be expressed by thecellular translation complexes or remain silent, or can be inhibitedusing an inhibitory nucleic acid as disclosed elsewhere herein. On day2, the same cell can be phototransfected again, transfecting one or moreof the same or dissimilar nucleic acids to the same cell. The presentinvention is not limited to phototransfection separated by a dayhowever. Sequential phototransfection can occur with minutes, hours,days, weeks or months between a first time point and a second timepoint, provided the phototransfection occurs to the same cell. Thus, thesequential phototransfection methods of the present invention arelimited only by the lifespan of the cell. Another non-limiting exampleof sequential phototransfections comprises a first phototransfection onDay 1, a second phototransfection 48 hours later (Day 3) and a thirdphototransfection 7 days after the first phototransfection. Theconditions of sequential transfection may be the same or different. Themeans of transfection may be changed and/or the number of sitestransfected in a transfection step may be different among multipletransfections. For instance, the second and subsequent transfectionsusing phototransfection may be performed using a reduced laser powercompared to the laser power used in the first phototransfection.

The sequential phototransfection methods of the present application areuseful for, among other things, analyzing temporal gene expression in acell, analyzing the multigenic effects of a protracted developmentalprocess, and determining the relationship of genotype to phenotype overthe course of the viable life span of a cell. Sequentialphototransfection using the same nucleic acids also increases therobustness of expression of the phototransfected nucleic acids. As shownherein, three sequential phototransfections of an astrocytetranscriptome into a neuron yields a durable phenotype conversion in ahigh percentage of neuron cells.

The embodiments of the inventions disclosed herein are not limited tomRNA. The present invention can further comprise reverse transcribingmRNA into cDNA, then transfecting the cDNA into a cell

The present invention is not limited to the use of RNA and mRNA. Amixture of DNA and RNA can be used in the methods of the presentinvention to determine the effects of transient (RNA) as well asprolonged (DNA integration into the genome) gene expression in a cell.

When a mixture of nucleic acids, such as a mixture of RNAs isphototransfected into a cell, subpopulations of that mixture can bephototransfected into a cell to determine the core set of RNAsresponsible for a given phenotype. As a non-limiting example, when thetotal RNA is isolated from a cell in a certain physiological state andmRNA is isolated from that population of total RNA, specificsubpopulations of the isolated mRNA can be transfected into a cell toestablish the core mRNAs responsible for that phenotype. The presentembodiment can also be performed with cDNA produced from mRNA. Specificpopulations of mRNA can be identified using sequence homology data orother characteristic features known in the art and available fromvarious databases, such as GenBank® (United States Department of Healthand Human Services, Bethesda Md.).

Alternatively, the mRNA from a cell can be isolated and transfected intoa cell using the methods of the present invention, and an siRNA,microRNA, antisense nucleic acid or ribozyme (collectively referred toas an inhibitory nucleic acid) can be transfected along with the mRNA,resulting in silencing and/or inhibition of an mRNA. Silencing an mRNApermits one of skill in the art to identify, for instance, the coremRNA(s) responsible for a multigenic phenotype. In addition, the presentinvention allows the replication of a phenotype in another cell withoutthe step of determining the nucleic acid expression profile of a cell ina physiological state. The nucleic acid, preferably RNA, from a cell ina specific physiological state, such as a certain differential ordisease state, can be isolated. Preferably, an mRNA transcriptome isthen isolated. Using the methods of the present invention, the RNA, or acDNA of the RNA, can be transfected into a cell in order to analyze thephenotype in the transfected cell once the nucleic acid has beenexpressed. The nucleic acid, preferably RNA, can be the total RNA from acell, or a subpopulation of the RNA, such as the mRNA transcriptome.

To assess the effect of expression of the transfected nucleic acids,cells transfected in accordance with the method of the invention can beexamined using methods known in the art. Assessments may be made, forexample, of phenotypic changes, mRNA expression, protein expression andfunctional assays. Examples of such analyses include, but are notlimited to, cell morphology, presence and absence of immunologicalmarkers, RT-PCR, expression profiling, mRNA abundance measurements,immunocytochemistry analysis (ICC) for specific proteins, cellviability, and cell-specific activities, such as cell division-mitosisand electrophysiology.

Optionally, the present method further comprises inhibitingtranscription factors in the transfected cell, thus preventingcompetition between expression of endogenous and exogenous mRNAs and theproteins encoded thereby. A transcription factor can be inhibited byaddition of exogenous agents, such as an inhibitory nucleic acid orcompounds that inhibit transcription factors, such as a protease, orSP100030 (Huang et al., 2001, Br. J. Pharmacol., 134: 1029-1036). Otheragents useful for inhibiting transcription in a recipient cell include,but are not limited to, α-amanitin, trichostatin A (TSA; a histonedeacetylase inhibitor), tubulin depolymerizer and actin depolymerizer.Preferably, a recipient cell is contacted with one or more transcriptioninhibition agents prior to transfection. Preferably, the cell iscontacted between about 30 minutes and about 80 hours, preferablybetween about 30 minutes and about 60 hours and more preferably, betweenabout 6 hours to about 48 hours, prior to transfection. In anon-limiting example, a rat hippocampal neuron is contacted with TSA andα-amanitin at a final concentration of 100 nM and 100 microgram per mlin a neuronal cell medium, respectively. The neuron is then irradiatedbetween about 24 to about 55 hours later. In some embodiments of theinvention including sequential phototransfection of a recipient cell,the recipient cell is preferably not contacted with a transcriptioninhibitor subsequent to the first phototransfection.

As shown herein, durable phenotype conversion is achievable withoutinhibition of transcription factors. Accordingly, in a preferredembodiment, the methods of the invention are practiced in the absence ofexogenous agents for transcription factor inhibition. “Exogenous agent”in this context excludes any inhibitors encoded by a transcriptome orpresent in the transcriptome from the donor cell.

FIG. 1A depicts a non-limiting example of a timeline forphototransfection of a recipient cell, for instance a neuron, withphenotype-converting nucleic acid, such as the mRNA transcriptome from adonor cell, for instance, a glial cell. The timeline depicts threesequential phototransfections in the complete absence of transcriptioninhibitor treatment, followed by a period of phototransfection cellrecovery and a period of cell remodeling and redifferentiation. Apossible change in growth media from a recipient-cell-specific medium toa donor-cell-specific medium is indicated after the firstphototransfection. Such media changes are useful, for instance, forsupporting phenotype conversion. Assays that may be used to characterizethe remodeling and redifferentiation of the phototransfected recipientcell are enumerated in the box on the top right.

The present method can also be used for the specific and localtransfection of an inhibitory nucleic acid, such as an siRNA, antisensenucleic acid or a microRNA (miRNA), using the methods of the presentinvention. Using the invention disclosed herein, the skilled artisan canspecifically inhibit a cellular nuclear acid, especially those incellular processes. Further, as disclosed elsewhere herein, aninhibitory nucleic acid can be used to identify the core nucleic acid(s)involved in a multigenic phenotype.

The phenotype-converting nucleic acids useful in the methods of thepresent invention may comprise a variety of nucleic acids, includingvarious species of RNA (mRNA, siRNA, miRNA, hnRNA, tRNA, total RNA,combinations thereof and the like) as well as DNA. Methods for isolatingRNA from a cell, synthesizing a short polynucleotide, constructing avector comprising a DNA insert, and other methods of obtaining a nucleicacid to phototransfect into a cell are well known in the art andinclude, for example, RNA isolation, cDNA synthesis, in vitrotranscription, and the like.

The nucleic acid compositions of this invention, whether RNA, cDNA,genomic DNA, or a hybrid of the various combinations, may be isolatedfrom natural sources or may be synthesized in vitro. Techniques fornucleic acid manipulation are described generally in Sambrook et al.(2001, Molecular Cloning: A Laboratory Manual, Cold Spring HarborLaboratory, New York), and in Ausubel et al. (1997, Current Protocols inMolecular Biology, John Wiley & Sons, New York)., incorporated herein byreference. Nucleic acids suitable for use in the present method alsoinclude nucleic acid analogs. Examples of such analogs include, but arenot limited to, phosphorothioate, phosphotriester, methyl phosphonate,short chain alkyl or cycloalkyl intersugar linkages, or short chainheteroatomic or heterocyclic intersugar (“backbone”) linkages. Inaddition, nucleic acids having morpholino backbone structures (U.S. Pat.No. 5,034,506) or polyamide backbone structures (Nielsen et al., 1991,Science 254: 1497) may also be used.

The methods of the present invention can comprise the use of a varietyof nucleic acids, including DNA, RNA, a cDNA reverse transcribed from anmRNA, an RNA transcribed from that cDNA, a DNA amplified from the cDNA,an RNA transcribed from the amplified DNA, and the like. The presentinvention further comprises using single-stranded and double-strandedRNA and DNA molecules. Any coding sequence of interest can be used inthe methods of introducing and translating a nucleic acid in a cell orin a cellular process, such as a dendrite. One of skill in the art willunderstand, when armed with the present disclosure, that a multitude ofproperties of a cellular process, and by association, of the attachedcell, can be affected by the methods of the present invention. Forinstance, for studies of dendrite remodeling, any coding sequence for aprotein involved in the growth, homeostasis or remodeling of a dendriteare useful in the methods of the invention. Non-limiting examples ofsuch proteins include: cadherin, neurexin, synaptophysin, tubulin,microtubule associated proteins and actin.

In one embodiment of the present invention, the nucleic acidphototransfected into a cell is all or a portion of the total mRNAisolated from a biological sample. The term “biological sample,” as usedherein, refers to a sample obtained from an organism or from components(e.g., organs, tissues or cells) of an organism. The sample may be ofany biological tissue or fluid. The nucleic acid (either genomic DNA ormRNA) may be isolated from the sample according to any of a number ofmethods well known to those of skill in the art.

Methods of isolating total mRNA are well known to those of skill in theart. For example, methods of isolation and purification of nucleic acidsare described in detail in Chapter 3 of Laboratory Techniques inBiochemistry and Molecular Biology: Hybridization With Nucleic AcidProbes, Part I. Theory and Nucleic Acid Preparation, P. Tijssen, ed.Elsevier, N.Y. (1993) and Chapter 3 of Laboratory Techniques inBiochemistry and Molecular Biology: Hybridization With Nucleic AcidProbes, Part I. Theory and Nucleic Acid Preparation, P. Tijssen, ed.Elsevier, N.Y. (1993)).

Preferably, the total nucleic acid is isolated from a given sampleusing, for example, an acid guanidinium-phenol-chloroform extractionmethod and polyA⁺ mRNA is isolated by oligo dT column chromatography orby using (dT)n magnetic beads. Commercially available products, such asTRIZOL and MICRO-FASTTRACK (Invitrogen™, Carlsbad, Calif.), are usefulin extracting nucleic acid from a biological sample.

The mRNA can be locally transfected directly into a cell or a cellularprocess, or the sample mRNA can be reverse transcribed with a reversetranscriptase and a promoter comprising an oligo dT and a sequenceencoding the phage T7 promoter to provide single stranded DNA template.The second DNA strand is polymerized using a DNA polymerase. Aftersynthesis of double-stranded cDNA, T7 RNA polymerase is added and RNA istranscribed from the cDNA template. Successive rounds of transcriptionfrom each single cDNA template results in amplified RNA. Methods of invitro polymerization are well known to those of skill in the art (see,e.g., Sambrook, supra.; Van Gelder, et al., 1990, Proc. Natl. Acad. Sci.USA, 87: 1663-1667). Moreover, Eberwine et al. (1992, Proc. Natl. Acad.Sci. USA, 89: 3010-3014) provide a protocol using two rounds ofamplification via in vitro transcription to achieve greater than 10⁶fold amplification of the original starting material.

The present invention further comprises the use of in vitrotranscription for phototransfection into a cell or cellular process. Invitro transcription comprises the production of dsRNA by transcribing anucleic acid (DNA) segment in both directions. For example, theHiScribe™ RNAi transcription kit (New England Biolabs, Ipswich, Mass.)provides a vector and a method for producing a dsRNA for a nucleic acidsegment that is cloned into the vector at a position flanked on eitherside by a T7 promoter. Separate templates are generated for T7transcription of the two complementary strands for the dsRNA. Thetemplates are transcribed in vitro by addition of T7 RNA polymerase anddsRNA is produced. Similar methods using PCR and/or other RNApolymerases (e.g., T3 or SP6 polymerase) can also be used and are knownin the art.

The present invention further comprises the use of chemicallysynthesized nucleic acids for use in phototransfection. Oligonucleotidesfor use as probes can be chemically synthesized according to the solidphase phosphoramidite triester method first described by Beaucage,(1981, Tetrahedron Letts., 22:1859-1862) using an automated synthesizer,as described in Needham-VanDevanter, et al. (1984, Nucleic Acids Res.,12:6159-6168). Purification of oligonucleotides is by either nativeacrylamide gel electrophoresis or by anion-exchange HPLC as described inPearson (1983, J. Chrom., 255:137-149). The sequence of the syntheticoligonucleotides can be verified using the chemical degradation methodof Maxam (1980, in Grossman and Moldave, eds., Methods in Enzymology,Academic Press, New York, 65:499-560).

The present invention can further comprise the use of DNA in a processto locally transfect a cell or a cellular process via phototransfection.The DNA can be contained in a vector, such as those described herein.

The invention includes an isolated DNA encoding a protein operablylinked to a nucleic acid comprising a promoter/regulatory sequence suchthat the nucleic acid is preferably capable of directing expression ofthe protein encoded by the nucleic acid. Thus, the invention encompassesexpression vectors and methods for the introduction of exogenous DNAinto cells with concomitant expression of the exogenous DNA in the cellssuch as those described, for example, in Sambrook et al. (2001,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory,New York), and in Ausubel et al. (1997, Current Protocols in MolecularBiology, John Wiley & Sons, New York).

Expression of a protein in a cell or a cellular process phototransfectedas disclosed herein may be accomplished by generating a plasmid or othertype of vector comprising the desired nucleic acid operably linked to apromoter/regulatory sequence which serves to drive expression of theprotein, with or without a tag, in cells in which the vector isintroduced. Many promoter/regulatory sequences useful for drivingconstitutive expression of a gene are available in the art and include,but are not limited to, for example, the cytomegalovirus immediate earlypromoter enhancer sequence, the SV40 early promoter, as well as the Roussarcoma virus promoter, and the like. Moreover, inducible and tissuespecific expression of the nucleic acid encoding a protein can beaccomplished by placing the nucleic acid encoding a protein under thecontrol of an inducible or tissue specific promoter/regulatory sequence.Examples of tissue specific or inducible promoter/regulatory sequenceswhich are useful for his purpose include, but are not limited to theMMTV LTR inducible promoter, and the SV40 late enhancer/promoter. Inaddition, promoters which are well known in the art which are induced inresponse to inducing agents such as metals, glucocorticoids, and thelike, are also contemplated in the invention. Thus, it will beappreciated that the invention includes the use of anypromoter/regulatory sequence, which is either known or unknown, andwhich is capable of driving expression of the desired protein operablylinked thereto.

Selection of any particular plasmid vector or other DNA vector is not alimiting factor in this invention and a wide plethora of vectors arewell-known in the art. Further, it is well within the skill of theartisan to choose particular promoter/regulatory sequences and operablylink those promoter/regulatory sequences to a DNA sequence encoding adesired polypeptide. Such technology is well known in the art and isdescribed, for example, in Sambrook et al. (2001, Molecular Cloning: ALaboratory Manual, Cold Spring Harbor Laboratory, New York), and inAusubel et al. (1997, Current Protocols in Molecular Biology, John Wiley& Sons, New York).

The nucleic acids encoding a protein can be cloned into various plasmidvectors. However, the present invention should not be construed to belimited to plasmids or to any particular vector. Instead, the presentinvention should be construed to encompass a wide plethora of vectorswhich are readily available and/or well-known in the art.

The present invention further comprises locally transfecting aninhibitory nucleic acid, such as an antisense nucleic acid, an siRNA oran miRNA via phototransfection into a cell. An siRNA polynucleotide isan RNA nucleic acid molecule that interferes with RNA activity that isgenerally considered to occur via a post-transcriptional gene silencingmechanism. An siRNA polynucleotide preferably comprises adouble-stranded RNA (dsRNA) but is not intended to be so limited and maycomprise a single-stranded RNA (see, e.g., Martinez et al., 2002, Cell110:563-74). The siRNA polynucleotide included in the invention maycomprise other naturally occurring, recombinant, or syntheticsingle-stranded or double-stranded polymers of nucleotides(ribonucleotides or deoxyribonucleotides or a combination of both)and/or nucleotide analogues as provided herein (e.g., an oligonucleotideor polynucleotide or the like, typically in 5′ to 3′ phosphodiesterlinkage). Accordingly it will be appreciated that certain exemplarysequences disclosed herein as DNA sequences capable of directing thetranscription of the siRNA polynucleotides are also intended to describethe corresponding RNA sequences and their complements, given the wellestablished principles of complementary nucleotide base-pairing.

An siRNA may be transcribed using as a template a DNA (genomic, cDNA, orsynthetic) that contains a promoter for an RNA polymerase promoter. Forexample, the promoter can be the U6 promoter or the H1 RNA polymeraseIII promoter. Alternatively, the siRNA may be a synthetically derivedRNA molecule. In certain embodiments, the siRNA polynucleotide may haveblunt ends. In certain other embodiments, at least one strand of thesiRNA polynucleotide has at least one, and preferably two nucleotidesthat “overhang” (i.e., that do not base pair with a complementary basein the opposing strand) at the 3′ end of either strand of the siRNApolynucleotide. In a preferred embodiment of the invention, each strandof the siRNA polynucleotide duplex has a two-nucleotide overhang at the3′ end. The two-nucleotide overhang is preferably a thymidinedinucleotide (TT) but may also comprise other bases, for example, a TCdinucleotide or a TG dinucleotide, or any other dinucleotide. Theoverhang dinucleotide may also be complementary to the two nucleotidesat the 5′ end of the sequence of the polynucleotide that is targeted forinterference. For a discussion of 3′ ends of siRNA polynucleotides see,e.g., WO 01/75164.

Preferred siRNA polynucleotides comprise double-stranded polynucleotidesof about 18-30 nucleotide base pairs, preferably about 18, about 19,about 20, about 21, about 22, about 23, about 24, about 25, about 26, orabout 27 base pairs, and in other preferred embodiments about 19, about20, about 21, about 22 or about 23 base pairs, or about 27 base pairs.The siRNA polynucleotide useful in the present invention may alsocomprise a polynucleotide sequence that exhibits variability bydiffering (e.g., by nucleotide substitution, including transition ortransversion) at one, two, three or four nucleotides from a particularsequence. These differences can occur at any of the nucleotide positionsof a particular siRNA polynucleotide sequence, depending on the lengthof the molecule, whether situated in a sense or in an antisense strandof the double-stranded polynucleotide. The nucleotide difference may befound on one strand of a double-stranded polynucleotide, where thecomplementary nucleotide with which the substitute nucleotide wouldtypically form hydrogen bond base pairing, may not necessarily becorrespondingly substituted. In preferred embodiments, the siRNApolynucleotides are homogeneous with respect to a specific nucleotidesequence.

Polynucleotides that comprise the siRNA polynucleotides may in certainembodiments be derived from a single-stranded polynucleotide thatcomprises a single-stranded oligonucleotide fragment (e.g., of about18-30 nucleotides) and its reverse complement, typically separated by aspacer sequence. According to certain such embodiments, cleavage of thespacer provides the single-stranded oligonucleotide fragment and itsreverse complement, such that they may anneal to form, optionally withadditional processing steps that may result in addition or removal ofone, two, three or more nucleotides from the 3′ end and/or the 5′ end ofeither or both strands, the double-stranded siRNA polynucleotide of thepresent invention. In certain embodiments the spacer is of a length thatpermits the fragment and its reverse complement to anneal and form adouble-stranded structure (e.g., like a hairpin polynucleotide) prior tocleavage of the spacer, and optionally, subsequent processing steps thatmay result in addition or removal of one, two, three, four, or morenucleotides from the 3′ end and/or the 5′ end of either or both strands.A spacer sequence may therefore be any polynucleotide sequence asprovided herein that is situated between two complementarypolynucleotide sequence regions which, when annealed into adouble-stranded nucleic acid, result in an siRNA polynucleotide.

The present method further comprises methods for introducing a nucleicacid into a cell. The method comprises phototransfecting a cell in thepresence of a nucleic acid, preferably RNA and/or DNA, where the nucleicacid is in a fluid medium permitting the transfer of the nucleic acidfrom one side of the cell membrane to the other side of the cellmembrane through a hole in the cell membrane. The fluid medium cancomprise any medium having the buffering capacity and pH to support theviability of a cell and the stability of a nucleic acid molecule.Contemplated media include, but are not limited to, phosphate bufferedsaline, Tris, Tris-EDTA (TE) cell culture media, other aqueous mediumsand buffers, and the like.

The number of nucleic acid molecules that enter the cell is influencedby the nucleic acid concentration in the nucleic acid bath, the size ofthe nucleic acid molecule, and laser intensity, e.g., the length of eachlaser pulse and the number of laser pulses delivered. Based on theteachings herein, the skilled artisan can readily adjust the parametersof the phototransfection process to control the approximate number ofnucleic molecules that enter the neuron per pulse.

In one embodiment, a cell is surrounded by an nucleic acid bathcomprising a nucleic acid molecule, preferably an RNA molecule, at about1 to about 150 μg/ml, more preferably about 10 to about 100 μg/ml, andmore preferably still at about 10 to about 50 μg/ml in the bath.Preferably the bath is in a container that is permeable by a laser anddoes not distort the beam, even more preferably, the bath is opticallyclear glass with a thickness of about 0.1 mm.

In another embodiment, a cell is bathed in discrete locations on thecell surface with a solution comprising a nucleic acid molecule. Forinstance, using a patch pipette, micropipette or other applicator, asolution comprising nucleic acid is applied to a discrete location onthe surface of a cell. The solution may be applied to more than onelocation on a cell. The cell is then irradiated using a laser at one ormore sites within a discrete location. Nucleic acid in the solution ispresent at about 1 nanogram per microliter (ng/μl) to about 2microgram/microliter (μg/μl), preferably about 50 ng/μl to about 1μg/μl, and more preferably about 100 ng/μl to about 500 ng/μl.

The present invention further comprises the use of other methods forintroducing a nucleic acid to a cell, tissue or animal viaphototransfection. Methods included in the present invention include,for example, perfusion, picospritzing, microinjection and the like.Methods for perfusion include, but are not limited to, using a pump tomove a fluid medium comprising a nucleic acid, preferably RNA, even morepreferably mRNA, to a cell, tissue or animal. The fluid medium used inthe perfusion methods of the present invention can included thosedisclosed elsewhere herein, such as buffered solutions that support andmaintain the stability of a nucleic acid and a cell, tissue or animal.In one embodiment of the present invention, the fluid medium can includea medium, such as Basal Media Eagle (BME), BGJb Medium, Brinster'sBMOC-3 Medium, CMRL Medium, CO2-Independent Medium, Dulbecco's ModifiedEagle Media (D-MEM), F-10 Nutrient Mixtures, F-12 Nutrient Mixtures,Glasgow Minimum Essential Media, Grace's Insect Cell Culture Media,Improved MEM, IPL-41 Insect Media, Iscove's Modified Dulbecco's Media,Leibovitz's L-15 Media, McCoy's 5A Media (modified), MCDB 131 Medium,Media 199, Medium NCTC-109, Minimum Essential Media (MEM), ModifiedEagle Medium (MEM), Opti-MEM® I Reduced Serum Media, RPMI Media 1640,Schneider's Drosophila Medium, Waymouth's MB 752/1 Media, Williams MediaE, artificial spinal fluid (aCSF), Ringer's solution and the like. Thepresent invention can further comprise the use of buffered saltsolutions, including, but not limited to, Dulbecco's Phosphate-BufferedSaline (D-PBS), Earle's Balanced Salt Solution, Hanks' Balanced SaltSolution, Phosphate-Buffered Saline (PBS), and the like.

The present invention further comprises using picospritzing inconjunction with phototransfection to introduce a nucleic acid to acell, organ or tissue. Picospritzing comprises the use of electricalpulses with a pressure device to deliver a compound, such as a nucleicacid, to a cell, tissue or animal. Method for picospritzing are known inthe art and are described in, for example, Herberholz, et al., 2002, J.Neuroscience, 22: 9078-9085). Picospritzing apparatuses are availablefrom, for example, World Precision Instruments (Sarasota, Fla.).

In another embodiment, transfection of cells with nucleic acids encodingtwo or more different polypeptides is effected by microinjection. Inthese embodiments, the recipient cell is preferably a somatic cell,preferably a somatic, differentiated cell.

The present invention comprises irradiating a cell with a laser tophototransfect and locally transfect the cell. When the laser contactsthe cell membrane, or cell wall in the case of plant cells, fungalcells, and other cells comprising a cell wall, the plasma membrane orcell wall is perforated, permitting the diffusion of foreign molecule,such as RNA and/or DNA, to enter the cell. The fluidity of mammaliancell membranes facilitates subsequent closure of the perforation. Laserscompatible with the present invention include, but are not limited to,continuous-wave argon-ion lasers operating at 488 nm (Schneckenburger,et al., 2002, J. Biomed. Opt., 7: 410-416; Palumbo et al., 1996, J.Photochem. Photobiol. B-Biol., 36: 41-46), pulsed and frequencyupconverted Nd:YAG lasers operating at 355 nm (Shirahata, et al., 2001,J. Invest. Med., 49: 184-190), 532 nm (Soughayer, et al., 2000, Anal.Chem., 72: 1342-1347), and 1064 nm (Mohanty, et al., 2003, Biotechnol.Lett. 25: 895-899), and femtosecond titanium-sapphire lasers (Tirlapur,et al., 2002, Plant J. 31: 365-374; Tirlapur, et al., 2002, Nature 418:290-291; Zeira, et al., 2003, Mol. Therapy 8: 342-350). Preferably, atitanium-sapphire laser at 405 nm (PicoQuant GmbH, Berlin Germany) isused to phototransfect a cell. However, the present invention is notlimited to the a titanium-sapphire laser, but includes any laser withthe capacity of delivering a localized focal volume of about 10¹⁹ m³.

Control of the incident laser beam is achieved by using variousapparatuses to control the focus and power of the laser, as well as toaim the laser. Focusing the laser is achieved by passing the incidentlaser through a lens, such as a microscope lens, placed between thelaser and the cell. The power of the laser in controlled by modulatingthe voltage and current going to the laser and through the use ofneutral density filters or pockels cells. Exposure of the cells to thelaser is controlled through a shutter, such as a single lens reflex(SLR) camera shutter and/or with electronically controlled pockelscells.

Aiming the laser is accomplished through a microscope lens and withdielectric and steering mirrors and AOD (acoustic optical deflector)between the laser source and a cell. A microscope useful in the practiceof the present invention includes, but is not limited to, a confocalmicroscope, a multiphoton excitation fluorescence microscope, a lightmicroscope, and the like. The present method further comprises aimingthe laser using an optical fiber to transmit the laser to a distant ordifficult-to-access area. As a non-limiting example, an optical fiber isused to phototransfect intestinal, neural or cardiothoracic cells in alive animal. Further, the present invention comprises phototransfectinga cell or a population of cells using multiple optical fibers in ananimal. Optical fibers are well known in the art and are described in,for example, U.S. Pat. Nos. 3,711,262 6,973,245.

A laser beam with less than a milliwatt of power for tens ofmilliseconds is sufficient to porate a cell (Paterson, et al., 2005,Optics Express, 13: 595-600). Preferably, the laser has a power densityof about 1200 MWm⁻² and a total power of about 30-55 mW at the backaperture of the lens. Further, in order to provide maximum surface areafor transfection, the laser beam should be highly circular (dx=dy) withbeam diameter of about 2 mm.

The starting power output of the laser is attenuated through the use ofvarious filters, such as a neutral density (ND) filter to reduce thepower to the milliwatt range required for phototransfection with noattendant pathological effects on the target cell. The beam can beexpanded through the used of a telescope where f=100 mm, and directedinto a microscope, such as a light microscope or an oil-immersionmicroscope with a ×100 objective (N.A.=1.25). An SLR shutter between thelaser source and the microscope permits control of the exposure time. Anexposure time of about 40 ms is sufficient to porate a cell withoutattendant damage, but this parameter can be altered to increase ordecrease exposure time.

Target cells in a nucleic acid bath are positioned and focused on bymanipulating the stage of the microscope and/or using dielectric andsteering mirrors and AOD, so the beam is focused on the cell membraneand not towards the nucleus of the cell. When porating a cellularprocess, such as a dendrite, the beam is focused directly on thecellular process.

An exemplary phototransfection protocol comprises at least two andpreferably three sequential phototransfection steps of a recipient cellusing the transcriptome, preferably the mRNA transcriptome, from a donorcell. The mRNA transcriptome comprises a range of mRNA sizes and has anaverage transcript size between about 1 to 3.5 kb. The firstphototransfection step is at about 35 mW using a titanium-sapphire laserand subsequent phototransfections steps are at a lower power, such as 30mW or less. Each phototransfection step involves laser irradiating therecipient cell at numerous, random sites. The number of sites per stepis determined by consideration of the strength of the laser, thediameter of the pores that result in the irradiated site, the averagesize of the transcripts in the mRNA transcriptome and modeling transportof individual transcripts through the pore using Brownian dynamics.After the first phototransfection step, the recipient cell may betransferred to a growth medium specific for the donor cell.

The cell or cellular process is irradiated with a laser according to theparameters disclosed herein. In one embodiment, the cells aretransfected with a nucleic acid comprising a marker that indicates asuccessful transfection. Such markers are known in the art and include,for example, antibiotic resistance and fluorescent proteins. Successfulporation can be tracked by the addition of a detectable molecule to thenucleic acid solution. Such molecules are well known in the art.Preferably, the molecule is non-toxic to the recipient cell.Non-limiting examples include Lucifer yellow and carboxyfluoresceindiacetate succinimidyl ester. The cells are incubated according to theincubation conditions prior to irradiation with the laser. Expression ofthe locally transfected nucleic acid is analyzed according to thepresence and activity of a marker or the phenotype of the cell.

EXAMPLES

The invention is further described in detail by reference to thefollowing experimental examples. These examples are provided forpurposes of illustration only, and are not intended to be limitingunless otherwise specified. Thus, the invention should in no way beconstrued as being limited to the following examples, but rather, shouldbe construed to encompass any and all variations which become evident asa result of the teaching provided herein.

The materials and methods used in Experimental Examples 1-6 below arenow described.

RNA Isolation, Amplification and Array Analysis:

Rat astrocytic transcriptome was extracted from the astrocyte cultureusing TRIzol® Reagent and Micro-FastTrack™ 2.0 Kit. The host hippocampalculture was prepared as previously described (Fukaya, et al. (2007)Arachidonic acid preserves hippocampal neuron membrane fluidity insenescent rats. Neurobiol Aging 28(8):1179-1186; Neufeld et al., (1985)Uptake and subcellular distribution of [3H]arachidonic acid in murinefibrosarcoma cells measured by electron microscope autoradiography. JCell Biol 101(2):573-581). After TIPeR, some coverslips were assessedusing standard calcium imaging and immunocytochemistry methods. The restof the samples were assessed using standard single-cell harvesting andaRNA amplification methods as previously described (Van Gelder et al.,(1990) Amplified RNA synthesized from limited quantities ofheterogeneous cDNA. Proceedings of the National Academy of Sciences ofthe United States of America 87 (5), 1663; Eberwine, et al., (2001)Analysis of mRNA populations from single live and fixed cells of thecentral nervous system. Current protocols in neuroscience/editorialboard, Jacqueline N. Crawley et al Chapter 5, Unit 5 3; and Eberwine,(2001) Single Cell Molecular Biology Nat Neurosci 4 Suppl, 1155-1156).For the final aRNA synthesis, the Ambion Illumina TotalPrep RNA Amp kitwas used, with an incubation time of 14 hours. The aRNA obtained fromindividual TIPeRed cells was used for nested RT-PCR to detect theexpression of GFAP and MAP2, and for Affymetrix Rat 230 2.0 analysiswhere a volume of 40 ul, containing 2 ug of aRNA.

Modeling Phototransfection Procedure:

The laser excitation pulse was assumed to form a transient permeabilityof the membrane, where the permeability had an exponential decay (t). Adistribution of membrane pore sizes was assumed to form in the area oflaser excitation (250 nm diameter of laser excitation), and the spot ofexcitation was moved in a random positional sequence, identical to thephototransfection process. Across 16 separate regions of the plasmamembrane, the phototransfection pulse produced a population of poreswithin the plasma membrane that would permit the transfer of dyes/mRNAsfrom the extracellular compartment to the cytosol. Although the exactpore size was not known, it was assumed that the distribution of poresizes was Gaussian, with separate simulations evaluating transportacross the plasma membrane for average pore sizes of 10 nm, 50 nm, 75nm, and 125 nm radius, based on estimates for stable pore sizes rangingfrom 1 nm-250 nm. Transport of individual transcripts through the porewas modeled using Brownian dynamics, accounting for the stericinteraction of the transcript with the pore by adjusting the freediffusivity of the transcript accordingly. Both entry and exit of thetranscript was accounted for by simulating molecular positions with 1microsecond timesteps.

Phototransfection:

A multiphoton scanhead attached to an Olympus BX61 fixed-stage uprightmicroscope equipped with a water-immersed 40× lens (LUMPlanFI/IR,numerical aperture (NA) 0.8) to monitor and mediate thephototransfection process. Two sets of galvanometer-controlled mirrorswere used independently for simultaneous imaging and phototransfecting.A transmitted light gradient contrast image was taken when the targetedneuron (DIV1) was found and the phototransfected area was selected andoutlined. A micropippette was backfilled with RNAs (200 ng/ul) mixedwith Lucifer yellow (LY) dye (Sigma, final concentration 0.5 mM). TheRNA mixture was ejected to the neuron using a Nanoject II tool (DrummondScientific Company). Once the Lucifer Yellow dye reached the maximalsaturation, indicating the highest RNA concentration surrounding theneuron, phototransfection was started using the titanium-sapphire laser(Mai-Tai, Spectral Physics). The titanium-sapphire laser created 16random transient poration sites within the outlined area by deliveringlaser pulses (˜100 femtosecond, 100 MHz) for 5 ms at a power of 35 mW(at the back aperture of the lens). The laser pulses were moved randomlyover the 16 sites with 5 ms interval between each pulse, which allowedthe RNA mixture to diffuse into the targeted neuron through thesetransient holes. The second and third phototransfection were performed48 hours and 7 days later, following the same procedure as describedabove, but with lower laser power (30 mW at the back aperture of thelens).

After phototransfection the cells were cultured in astrocyte mediumsupplemented with arachidonic acid and Dharmafect3 to bolster host celllipid composition during the TIPeR-induced remodeling of cellularphenotype (Fukaya T, et al. (2007) Arachidonic acid preserveshippocampal neuron membrane fluidity in senescent rats. Neurobiol Aging28(8):1179-1186; Neufeld E J, Majerus P W, Krueger CM, & Saffitz J E(1985) Uptake and subcellular distribution of [3H]arachidonic acid inmurine fibrosarcoma cells measured by electron microscopeautoradiography. J Cell Biol 101(2):573-581).

Immunocytochemistry:

Coverslips with cultured cells were fixed using 4% paraformaldehyde,then permeabilized using 0.2% triton-X for 15 min at room temperature.Endogenous biotin was blocked using the endogenous biotin blocking kit(Molecular Probe). Cells were blocked in 10% normal goat serum and 3%BSA for 1 hour at 37° C. Coverslips were then incubated using a mouseantibody against GFAP (1:250, Abcam) for 1 hour at 37° C., followed byincubation with goat anti-mouse secondary antibody conjugated with Alexa546 (1:500, Molecular Probe) for 8 minutes at 37° C. Coverslips wereagain immunolabeled using a mouse antibody against NeuN (1:50, Abcam)for 1 hour at 37° C., followed by incubation with goat anti-mousesecondary antibody conjugated with Alexa 488 (1:500, Molecular Probes)for 8 minutes at 37° C. Lastly, fibronectin immunoreactivity wasdetected using a rabbit antibody against fibronectin (1:250, Abcam) for1 hour at 37° C., followed by incubation with goat anti-rabbit secondaryantibody conjugated with Alexa 647 (1:500, Molecular Probe) for 8minutes at 37° C. Coverslips were finally mounted using Vectashield withDAPI (Vector Labs). Expression of GFAP, NeuN and fibronectin wasdetected using a confocal microscope (LSM 510, Carl Zeiss).

Calcium Imaging:

Calcium imaging was performed on an Olympus Fluoview FV1000 unit with anIX81 motorized inverted confocal microscope using a 20× lens (0.7 NA) atroom temperature. Cells were loaded with Fluo-4AM (10 μM, Sigma) for 50minutes at room temperature. Intracellular calcium changes wereconstantly imaged in 3-second intervals throughout. For analysis, regionof interest were selected based on reference DIC image of cells, whichwere taken during the TIPeR procedure, over gridded coverslips.Background subtracted fluorescent signal intensity (AF/F) was used toevaluate physiological responses. Due to the low level of signalintensity, 5 consecutive images were integrated for analysis. Thethreshold for responses was set for 5% of changes and compared to thesignals before and during drug applications. Image processing wasperformed using MetaMorph and Sigmaplot.

Single Cell Nested RT-PCR:

Primer sequences used for PCR (listed in order of forward primer andreverse primer) included:

GFAP outer (SEQ ID No. 1: 5′-AGTGGCCACCAGTAACATGCAA-3′;SEQ ID No. 2: 5′-TTGTCTTGCTCCAGCAGCCTAT-3′) and GFAP inner(SEQ ID No. 3: 5′-AGAAACCAGCCTGGACACCAAA-3′;SEQ ID No. 4: 5′-TGGGAATTGGGCCTAGCAAACA-3′), and MAP2 outer(SEQ ID No. 5: 5′-ATGGCCACCAAGACCTTGGAAA-3′;SEQ ID No. 6: 5-′ACGGACTTTGTCATCGGTTCCT-3′) and MAP2 inner(SEQ ID No. 7: 5′-TGGAGGGCAAACTACCCAAGTT-3′;SEQ ID No. 8: 5′-ATCAGCAACAGGTGGCAAACCA-3′).

For the templates, cDNAs for each sample were synthesized using 1 μl ofthird-round aRNAs with random hexamer and SuperScript III reversetranscriptase (Invitrogen). A total number of 45 cycles of amplificationwas used with an annealing temperature at 57° C. (first round) and at60° C. (second round). The final PCR products were examined using 2%agarose gel electrophoresis and then cloned into pCR2.1-TOPO vectorusing TOPO® TA Cloning Kit (Invitrogen). Sequences of the cloned PCRproducts were determined against nr nucleotide database at the NCBIwebsite using BLAST search algorithm.

Computational analysis of single-cell transcriptome: Analysis involvedseveral aspects: i) transcriptome quantification; ii) bootstrap clusteranalysis; iii) delineation of gene sets of biological interest; iv)visualization of transcriptome space; and v) Trans-activation of genesby donor astrocyte RNA.

i) Transcriptome Quantification.

For each single-cell transcriptome microarray measurements, probes withpervasive low quality measurements were removed (as reported byAffymetrix MAS 5.0) for all samples, in order to account for bothbackground expression variability. Genes related to thephototransfection effect were also removed, by selecting genes thatdifferentiate the N-TIPeR-N cells from the neurons (using Welch'st-test). Probe set expression intensities were background correctedusing the Robust Multichip Average algorithm (Bolstad B M I R, AstrandM, Speed T P (2003) A comparison of normalization methods for highdensity oligonucleotide array data based on variance and bias.Bioinformatics), quantile normalized, and summarized using anupper-decile statistic, as implemented in the Bioconductor packageaffyPLM (Gentleman R C, et al. (2004) Bioconductor: open softwaredevelopment for computational biology and bioinformatics. Genome Biol5(10):R80; Bolstad B M I R, Astrand M, Speed T P (2003) A comparison ofnormalization methods for high density oligonucleotide array data basedon variance and bias. Bioinformatics). The quality control resulted in3104 most informative genes for characterizing the cells.

ii) Bootstrap Cluster Analysis.

The single-cell transcriptome was clustered based on the Euclideandistances between their expression profiles using the standardUnweighted Pair Group Method with Arithmetic mean (UPGMA) clusteringmethod. To assess the robustness of the clusters, a set of 1000bootstrap datasets were generated by resampling the 3104 informativegenes with replacement, recomputing a UPGMA cluster tree for each andthen computing a consensus tree using PHYLIP (Felsenstein J (PhylogenyInference package Seattle), 3.6). For each cluster in the consensustree, the number of times that each putative cluster was found in the1000 re-sampled data sets was counted.

iii) Delineating Gene Sets of Biological Interest.

Within our informative set of 3104 genes, different gene sets ofbiological interest were isolated by contrasting astrocytes againstneurons. Gene sets that best discriminate a biological contrast ofinterest were identified by performing a Welch's t-test for each geneand extracting top 10% significantly differentially expressed genes withat least a two-fold average expression differential. Gene sets thatcontrast the following biological conditions were extracted: astrocytevs neurons (630 genes); astrocyte vs astro-TIPeR (136 genes); neurons vsastro-TIPeR (43 genes); and astro-TIPeR vs neuro-TIPeR (560 genes). Wealso generated A set of significantly similar gene groups betweendifferent cell types was generated using top 10% similar genes with theWelch's t-test statistic: astrocyte equals astro-TIPeR (69 genes);neuron equals astro-TIPeR (46 genes); and astro-TIPeR equals neuro-TIPeR(370 genes).

iv) Visualizing Transcriptome Space.

To generate each axis shown FIG. 4B, the gene sets from each biologicalcontrast of interest were used and each partition was summarized by theprincipal direction of variation foe each gene set. For the overallvariability axis, the principal direction of variation for the entireset of cell samples was generated.

v) Trans-Activation of Genes by Donor Astrocyte RNA.

To select for genes that have significantly low expression in bothastrocytes and neurons, for each of the 3104 informative genes, Fisher'scombined P-value was computed for their expression rank in the 8(neurons)+8 (astrocyte)=16 single-cell transcriptomes. The resultingp-values were multiple-test corrected for 3104 genes using Bonferronicorrection and cutoff at the 5% significance level, which left 171significantly low expressed genes. To assess significant up-regulationof these genes in 1 wk (9 cells), 2 wks (7 cells), 4 wks (11 cells), andN-TIPeR-N control cells (5 cells), pair-wise Welch's t-tests was carriedout for increased expression for each of these cell types against thecombined group of 16 astrocyte plus neurons. This analysis resulted in49, 17, 24, and 0 significantly up-regulated genes at p<0.05 level for 1week, 2 weeks, and 4 weeks TIPeRs, respectively, compared to theastrocytes and neurons. There were no (zero) significantly up-regulatedgenes at p<0.05 level for N-TIPeR-N controls, compared to the astrocytesand neurons.

The experimental results are now presented.

Experimental Example 1: Modeling of the Phototransfection of Complex RNAPopulations

To evaluate whether the astrocyte transcriptome can directly converthost neurons into astrocytes, the cell cultures were characterized toensure the purity of the neurons that were to be transfected. A mixedculture (DIV 9) and a typical neuronal culture (DIV 2) weredouble-labeled using an antibody to microtubule-associated protein 2(MAP2), which is a neuronal marker, and to glial fibrillary acidicprotein (GFAP), which is an astrocyte marker. The data revealed thatmixed cultures were immunoreactive for both MAP2 and GFAP. Notably, theyoung neuronal cultures were immunoreactive only for MAP2; thesecultures were used in the subsequent TIPeR experiments below.

A TIPeR protocol was established which involved multiple RNAphototransfections over a 10-day period of time (FIG. 1A).Phototransfection was selected as the means to transfect the astrocytetranscriptome into neurons as it can transfect RNA into neurons withhigh efficiency (Barrett L E, et al. (2006) Region-directedphototransfection reveals the functional significance of a dendriticallysynthesized transcription factor. Nat Methods 3(6):455-460). To optimizefor the amount of RNA that can be introduced into the host cells, thephototransfection of RNA transcripts that diffuse into the photoinducedpores in the cell membranes was modeled (FIGS. 2A and 2B). The processwas modeled with an average transcript size of 1.5 kb+/−0.2 kb with theeffective radius of the transcript determined by the Flory approximation(R_(transcript)˜5.5N^(1/3), where N is the size of the transcript inbases). Pore sizes were systematically varied to test the relative fluxof transcriptome in a typical phototransfection experiment.

Simulations with the approximated transcriptome cargo revealed that asingle sequence of sixteen pulses across the cell membrane would besufficient to deliver a large number of transcripts while retainingtheir relative abundances (FIGS. 1B and 1C). There is a slight reductionin delivery efficiency of the largest transcripts expected, as theirsizes are on the order of the assumed size of the phototransfectionpore. For a transcriptome that contains a large range of transcriptsizes, simulations indicated that the relative composition of thedelivered cargo to the cytosol would remain largely remain intact. Basedupon this simulation and empirical tests, 200 nanogram per microliter(ng/μl) concentration of poly-A+-selected RNA was used in theseexperiments. This is estimated to result in 160,000 transcript moleculesbeing delivered into the TIPeR cells in each phototransfection session;this number of transcripts is in excess of the normal contingent of mRNAtranscripts of a hippocampal neuron (˜100,000 molecules).

Experimental Example 2: Astrocyte mRNA TIPeRed Neurons Stably ExpressDonor Specific Astrocytic Markers

Neuron cells transfected with astrocyte RNA are designated hereinN-TIPeR-AS. The expression of the astrocytic marker GFAP and theneuronal marker MAP2 was assessed in the neurons TIPeRed with theastrocyte transcriptome. The individual N-TIPeR-AS cells were harvestedat three time points (1, 2 and 4 weeks) following the thirdphototransfection (FIG. 1A). Nested single cell RT-PCR and sequenceverification was then performed to assay GFAP and MAP2 mRNAs. Data inFIG. 3 show that 10 out of 26 N-TIPeR-AS cells across 4 weeks post-lastphototransfection displayed GFAP gene expression. A subset of the GFAPexpressing N-TIPeR-AS cells (8 cells) also expressed the neuronal MAP2mRNA, suggesting that these cells were intermediate between neuronal andastrocytic phenotypes. Finally, two cells showed no detectable MAP2 geneexpression in the RT-PCR assay, showing that MAP2 gene expression hadbeen turned off in these two cells.

The N-TIPeR-AS cells were also assessed for expression of astrocyticprotein markers. Triple-labeled immunocytochemistry was performed on theN-TIPeR-AS cells, using antibodies against the neuronal marker NeuN andthe astrocytic marker GFAP. Also used was an antibody against the higherabundance astrocytic marker fibronectin, which is the seventh mostabundant mRNA relative to GFAP, which is the 191^(st) most abundantmRNA, as observed in single astrocyte microarray analysis. Nofibronectin mRNA or protein was detected in neurons. Immunocytochemicalanalysis of NeuN, GFAP and fibronectin in N-TIPeR-AS cells two weeksafter the last phototransfection showed that astrocytic markers GFAP andfibronectin co-expressed with the neuronal marker NeuN (FIG. 3B). GFAPprotein expression was low, while fibronectin was more abundant in thesecells. Similar to the RT-PCR results, the N-TIPeR-AS cells co-expressionof all three antigens suggests that the 2-week N-TIPeR-AS cells were atan intermediate phenotypic state between neurons and astrocytes. Adistinct set of immunocytochemistry studies was also performed with theneuronal specific anti-Dynamin 1 antibody and anti-GFAP. To assess theexpression levels, the integrated fluorescence signal strength oftargeted cell area was analyzed (FIG. 3C). The results showed that theexpression patterns of Dynamin 1 and GFAP of TIPeR cells were similar tothat of astrocytes, while neurons had a distinctive pattern.

Experimental Example 3: N-TIPeR-AS Cells Display Global Alteration inOverall Gene Expression Profile

Single-cell transcriptomes of neurons, astrocytes, control cells(neurons TIPeRed with neuron transcriptome; designated as N-TIPeR-N),and N-TIPeR-AS cells were assayed for gene expression. RNA from 48individual cells was individually isolated, amplified, and assayed withAffymetrix Rat Genome 230 2.0 GeneChips.

FIG. 4A shows a cluster diagram of the single-cell transcriptomes for aset of 3104 informative genes and the bootstrap support of the clusters.Out of 27 N-TIPeR-AS cells, 12 (44%) cells consistently clustered withthe astrocytes 91% of the time, indicating expression profiles similarto the normal variation in astrocytes. These 12 TIPeR cells aredesignated herein as astro-TIPeRs, while the other 15 N-TIPeR-AS cellsthat do not cluster with the astrocytes are designated herein asneuro-TIPeRs. Control cells (N-TIPeR-N) were distinct from astrocyteswith only 3% of the bootstrap samples clustering control cells withastrocytes.

FIG. 4B shows a 3-dimensional projection of the 3104-gene transcriptomealong three biologically meaningful directions: (1) genesdifferentiating astrocytes and neurons; (2) genes showing largeN-TIPeR-AS variation; and (3) genes that are most variable in all cells.This 3-dimensional plot shows how the transcriptome of individual cellsdelimit variable but a distinct region of identity for each cell types(lightly shaded cloud around the composite cells). Any cell within thisregion of identity is classified phenotypically as the same cell type.The N-TIPeR-AS cell transcriptomes were measured at 1 week, 2 weeks, and4 weeks after the third photo-transfection. Interestingly, 3/9 of the1-week cells, 4/7 of the 2-week cells, and 5/11 of the 4-week cells fellinto the astro-TIPeR category, thus exhibiting an increasing astrocyticconversion (30% to 50%) between 1 and 2 weeks post-transfection age(FIG. 4A).

Experimental Example 4: De Novo, Up- and Down-Regulation of Genes areSeen in TIPeR Cells

To dissect the genes that differentiate successful TIPeR cells, pairedcomparisons were carried out between astro-TIPeR cells, neurons, andastrocytes. A total of 532 genes significantly distinguish neurons fromastrocytes with at least 2-fold intensity difference. These 532 genesseparated into four categories: (A) TIPeR expression=astrocytes neurons(201 probes), (B) TIPeR expression=neurons astrocytes (202 probes), (C)intermediate TIPeR expression (77 probes), and (D) TIPeR expressiondifferent from both neurons and astrocytes (32 probes). See FIG. 4C. AGO enrichment analysis was carried out to assess the functionalsignificance of the four groups (FIG. 5).

The up-regulated genes in group (A) showed greatest enrichment in thetranscriptional activity category (RNA Pol II activity, RNA metabolicprocess, nucleic acid binding, gene expression), while thedown-regulated genes were most enriched in the cell division andcytokinesis categories, as well as transmembrane transporter activity.It should be noted that down-regulated cell division genes do not meanthat cell division itself is inhibited in successful TIPeR cells (cf.,p53's activity in cell proliferation). Group (B) genes represent genesthat have failed to move towards astrocytes. These genes are enrichedfor glutamine metabolic process, spindle pole and chromosomes(up-regulated), as well as anti-oxidant pathways (down-regulated). Ofthe genes whose TIPeR expression is neither astrocyte-like norneuron-like (group C), notable enrichment of intra-cellularmembrane-bound organelle related processes were found.

Since the half-life of GFAP mRNA is 4 hours (Valles S, Pitrach J,Renau-Piqueras J, & Guerri C (1997) Ethanol exposure affects glialfibrillary acidic protein gene expression and transcription during ratbrain development. J. Neurochem 69:2484-2493), the GFAP gene expressionin N-TIPeR-AS cells at 4 weeks post-phototransfection (FIG. 3A)indicates that the GFAP gene was de novo trans-activated and thatendogenous GFAP mRNA was made, as also seen by the changes in globalgene expression (FIG. 4C). No de novo up-regulation is seen in controlcells.

To further confirm trans-activation of genes by donor RNA, genes whoseexpression level was significantly low in both neurons and astrocyteswere delineated. If any of these genes shows increased expression inN-TIPeR-AS cells distinct from control TIPeR cells, that result wouldindicate de novo up-regulation. Out of the 3104 informative genes, 171genes were found that were quiescent in both neurons and astrocytes(p<0.05). For each of these genes, significant up-regulation (p<0.05)was tested in 1-week (n=9), 2-week (n=7), 4-week (n=11) N-TIPeR-AScells, and in N-TIPeR-N control cells (n=5), respectively, against theastrocytes and neurons (n=16). Significant up-regulation was found for49 (1 wk), 17 (2 wk) and 24 (4 wk) genes in N-TIPeR-AS cells and none inN-TIPeR-N control cells (FIGS. 4D and 5). The 1 wkpost-phototransfection N-TIPeR-AS cells showed the greatest number ofsignificantly up-regulated genes. Since genes that are quiescent in theoriginal astroctye transcriptome were selected, the expression of thesegenes was expected to decrease in the N-TIPeR-AS cell with maturation ofthe re-programming process. This prediction was confirmed in 2 wk and 4wk N-TIPeR-AS cells (FIG. 4D). Interestingly, GO ontology annotationsuggests that the de novo up-regulated genes were enriched forchromosome and DNA metabolism related processes (FIGS. 6 and 7)indicating a chromosomal remodeling response to donor RNA. The set of3104 informative genes already excluded genes involved inphototransfection-specific systemic effects, and no de novo upregulationin N-TIPeR-N controls was found. These results are consistent withtransient up-regulation of a subset of genes soon after the introductionof new RNA, putatively induced by trans-factors translated from thedonor RNA.

Experimental Example 5: Morphological Analysis of TIPeRed Cells

The morphology of the N-TIPeR-AS cells was assessed using MetaMorphsoftware (Molecular Devices). The N-TIPeR-AS cells exhibited asubstantial reduction in cellular size (72% reduction from initial cellsize, n=27), including both soma and retained processes (FIG. 8B).Control N-TIPeR-N cells showed a smaller reduction in overall size whencultured in neuronal medium (21%, n=15) or when cultured in astrocytemedium (39%, n=29). In addition, there was a significant retraction ofprocesses in the N-TIPeR-AS cells that was not observed in N-TIPeR-Nneurons grown under either culture conditions. Data shown in FIG. 8Cillustrates that over 60% of the N-TIPeR-AS cells retracted allprocesses, whereas only 12% and 37% of N-TIPeR-N control cells culturedin astrocyte medium and neuronal medium, respectively, show retractedprocesses morphologies. Thus, the astrocyte transcriptome appears toinduce both a size reduction and a dramatic loss of the neuron-criticalprocesses. The different morphological effects of the neuronal andastrocyte transcriptomes upon the same host cell type (hippocampalneuron) highlight the transcriptome specific effects. The N-TIPeR-AScells showed a morphology that is smaller than that of a prototypicalastrocyte. The culture conditions likely contribute to the observedmorphology, as it is likely that re-plating after phototransfectionwould permit unconstrained membrane remodeling (Hanna J, et al. (2007)Treatment of sickle cell anemia mouse model with iPS cells generatedfrom autologous skin. Science 318(5858):1920-1923).

Experimental Example 6: N-TIPeR-AS Cells Display Astrocyte-LikePhysiological Responses

Cellular physiology results from the coordinate expression and functionof multiple gene products. Given that the microarray data (FIG. 4)indicate the development of an astrocyte-like expression profile in theN-TIPeR-AS cells, it is useful to determine if this global change ingene expression results in an astrocyte-like physiology. Intracellularcalcium plays an important role in physiological processes, and imagingof changes in intracellular calcium levels has been used to characterizeunique neuronal and astrocytic physiologies (Rowe E W, Jeftinija D M,Jeftinija K, & Jeftinija S (2005) Development of functional neurons frompostnatal stem cells in vitro. Stem Cells 23(8):1044-1049). Both neuronsand astrocytes express glutamate receptors and show increasedintracellular calcium when exposed to glutamate. Astrocytes, unlikeneurons, do not show rapid calcium increases upon KCl application.

As illustrated in FIG. 9, prior to TIPeR, 100% of the cells identifiedas neurons (25 out of 25 cells; designated pre-N-TIPeR-AS) displayedneuronal activity (calcium increases in response to both glutamate (500μM) and KCl (50 mM) application). The percentage of cells with neuronalresponses decreased to 33% (16 out of 48 cells) at 1 week, 22% (13 outof 58) at 2 weeks and 26% (11 out of 42) at 4 weeks after TIPeR. Cellsdisplaying astrocyte-like activities (calcium increases only uponglutamate, but not KCl application) grew from 0% (0 out of 25 cells)before TIPeR to 6% (3 out of 48 cells) after 1 week, 31% (18 out of 58cells) after 2 weeks and 36% (15 out of 42 cells) after 4 weeks. At theinitiation of the TIPeR process, all the cells expressed hostneuron-like physiological responses; with the passage of time, thenumber of N-TIPeR-AS cells showing neuron-like physiology decreased. Asthis decrease occurred, a population of cells that was physiologicallyundefinable as neurons or astrocytes became prominent at one week andthen receded, as the number of physiologically astrocyte-like cellsincreased. This indeterminate physiology may represent the initialresponse of the neuronal hosts to TIPeR, which is also seen asNeuro-TIPeR cells in the microarray data (FIGS. 4A and 4C). These datasuggest that the astrocyte-like physiology of the N-TIPeR-AS cellsincreases as a function of time post-phototransfection, in accord withthe progression seen in the single cell RT-PCR and single cellexpression profiling data.

Experimental Example 7: Preparation of Cardiomyocyte-Like Cells fromEmbryonic Fibroblasts

Cardiomyocyte-like cells (“tCardiomyocytes”) were created from mouseprimary embryonic fibroblasts using the following materials and methods.

Cells:

Mouse Primary Embryonic Fibroblast (PMEF) was purchased from MilliporeCorporation (Catalog number PMEF-NL) and incubated in Dulbecco'sModified Eagle Medium (DMEM) (Invitrogen) supplemented with 10% of fetalbovine serum (FBS) in the incubator (5% CO2, 37° C.).

Primary cardiomyocyte cells were prepared from heart ventricles of mouseand frozen at −80° C.

mRNA Isolation:

Total RNAs were isolated from frozen mouse cardiomyocytes using TRIzol®Reagent (Invitrogen) and chloroform following manufacturer's protocol.mRNAs were extracted from the total RNA using Micro-FastTrack™ 2.0 mRNAisolation Kit (Invitrogen). Isolated mRNA was quantified using aNanoDrop spectrophotometer (Thermo Scientific). RNA integrity wasexamined using a 2100 BioAnalyzer (Agilent).

Transfection:

Mouse cardiomyocyte mRNA was transfected into PMEF using TransMessengerTransfection Reagent (Qiagen, Valencia, Calif.). In brief, 2 μg of mRNAwas mixed with 4 μL of Enhancer R and then 8 μL of TransMessengerreagent was added to the mRNA-Enhancer R mixture. TransMessenger-mRNAcomplex was incubated with PMEF for 1 to 4 hours and washed. For mocktransfection, an equal amount of yeast transfer RNA was used instead ofcardiomyocyte mRNA. After the initial transfection, cells were culturedfor 2 days and retransfected in the same manner. Immunocytochemistry wasperformed on the cultures 1 week, 2 weeks and 3 weeks post-firsttransfection.

Cell Culture:

Transfected cell cultures were incubated in 10% FBS-DMEM with 50 μM ofPaclitaxel (Sigma-Aldrich) in a CO2 incubator.

Immunocytochemistry:

Cardiomyocyte marker antibodies were purchased from commercial vendors:anti-MyoD1 antibody (Abcam); anti-connexin43/GJA1 Ab (Abcam);anti-Nkx2.5 Ab (Abcam); and anti-cardiac Troponin I (Abcam).

Cells grown on glass-coverslips were fixed in 4% paraformaldehyde andpermeabilized using 0.1% Triton X-100 in phosphate buffer saline. Thecardiomyocyte marker antibodies were used in accordance withmanufacturer's recommendation and hybridized at 4° C. for overnight.Alexa Fluor secondary antibodies (Invitrogen) were used to detectprimary antibodies.

Cells were DAPI stained in accordance with a conventional protocol.

Imaging:

Zeiss LSM 5 confocal microscope system was used to take fluorescenceimages. Images were processed using MetaMorph® software (MolecularDevices, Silicon Valley, Calif.).

The results of this example are now discussed.

The TIPeRed MEFs expressed muscle-specific antigens, including MyoD,Connexin43 and Troponin-1. See FIG. 10. The expression was localized inthe appropriate cellular location. MyoD is a transcription factor thatis expressed in cardiomyocytes which functions to direct the muscle celldevelopment. Connexin 43 is a protein whose expression is enriched innative cardiomyocytes; it is involved in cardiac cell cytoarchitecture.Notably, tCardiomyocytes were observed to beat (e.g., rhythmicallycontract), as healthy, native cardiomyocytes do. In this experiment,approximately 5% of the cells were observed to convert totCardiomyocytes.

Additional characterization of tCardiomyocytes will include one or bothof the following: single cell microarray analysis on the TIPeRed cells,native cardiomyocytes and MEFs to ascertain the expression profilesimilarities and differences; and quantitative assessment of the abilityof these cardiomyocyte-like cells to contract in response tostimulation, which is one of the physiological characteristics ofcardiac muscle cells.

Experimental Example 8: Knock Out of CBP300 Using CRE Recombinase

An experiment was designed to assess whether individual genes could beknocked out in individual cells.

Mice engineered to have lox P sites flanking CBP300 were obtained fromTed Abel, University of Pennsylvania, Department of Biology. Cells wereobtained from the mice by dissociation of the hippocampus as describedin Buchhalter et al. (1991, Brain Res Bull. 26(3):333-338) and cultured.mRNA encoding CREe-recombinase was prepared by in vitro transcriptionfrom a Cre-recombinase cDNA-containing plasmid.

CRE-recombinase mRNA was introduced into individuals cells bylipid-mediated transfection, substantially as described in ExperimentalExample 7, with the exception that cells were transfect only once. Inthis experiment, two different concentrations of mRNA were used fortransfection: 4.5 micrograms mRNA/250 microliter of TransMessenger Lipidand 45 micrograms RNA/250 ul of TransMessenger Lipid. CBP expression wasevaluated in the nucleus of transfected cells by fluorescence microscopyat different times after transfection.

CBP expression was expected to completely disappear at some time afterCRE recombinase mRNA translation. However, the rate and time ofdisappearance of CBP protein is expected to be affected by severalfactors, such as amount of intrinsic level and stability of CBP proteinand mRNA. Furthermore, the amount of time needed for CRE recombinase toknockout the CBP gene is not known.

The results of this preliminary experiment suggest that this method wassuccessful in excising a gene of interest from chromosomal material.Specifically, at 48 hours post-transfection, a distinct segregation ofcells based on fluorescence intensity was not detected. However, at 7days post-transfection, a difference between the transfected cells andnon-transfected cells was observed. Images of representive cells areshown in FIG. 11. The extent of transfection was affected by the amountof mRNA used in the transfections. More transfected cells were observedfor the higher quantity of RNA; these data are on the far left in FIG.11. Lipid-mediated transfection is not an optimal transfection methodbecause of limitations such as non-specific and uncontrollabletransfection dosage. The knock out procedure described here is thusexpected to benefit from the preferred method of transfection,phototransfection.

These data support that the method can be used successfully to prepareindividual cells with a knock out, without requiring inducible promotersand their cognate inducers.

The disclosures of each and every patent, patent application, andpublication cited herein are hereby incorporated herein by reference intheir entirety.

While the invention has been disclosed with reference to specificembodiments, it is apparent that other embodiments and variations ofthis invention may be devised by others skilled in the art withoutdeparting from the true spirit and scope of the invention. The appendedclaims are intended to be construed to include all such embodiments andequivalent variations.

1. A method of effecting phenotype conversion in a cell, said methodcomprising transfecting phenotype-converting nucleic acid of a firstcell having a phenotype into a second cell having a phenotype, whereinthe phenotype of said first cell is different from the phenotype of saidsecond cell, and wherein said transfected phenotype-converting nucleicacid causes the phenotype of said second cell to change to the phenotypeof said first cell.
 2. The method of claim 1, wherein saidphenotype-converting nucleic acid is an mRNA transcriptome.
 3. Themethod of claim 1, wherein said phenotype of said first cell differsfrom said phenotype of said second cell by one or more of: species,tissue type, differentiation degree, disease state, exposure to a toxin,exposure to a pathogen, and exposure to a candidate therapeutic.
 4. Themethod of claim 1, wherein said mRNA transcriptome comprises mRNAtranscripts having an average size between about 1 kb to about 5 kb. 5.The method of claim 1, further comprising transfecting said second cellat least a second time with said first cell mRNA transcriptome.
 6. Themethod of claim 1, wherein said transfecting step comprises irradiatingsaid cell with a laser, wherein said cell is bathed in a fluidcomprising said first cell mRNA transcriptome.
 7. The method of claim 6,wherein said irradiating step comprises 2 to 25 laser excitation pulses,wherein said laser is directed to different site on said second cell foreach laser excitation pulse.
 8. The method of claim 1, wherein saidsecond cell is contacted with an exogenous transcription inhibitionagent prior to said transfecting step.
 9. The method of claim 1, whereinsaid second cell is not substantially contacted with an exogenoustranscription inhibition agent before, during or after said transfectingstep.
 10. The method of claim 1, wherein said cell is selected from thegroup consisting of a eukaryotic cell and a prokaryotic cell.
 11. Themethod of claim 10, wherein said eukaryotic cell is a non-mammaliancell.
 12. The method of claim 10, wherein said eukaryotic cell is amammalian cell.
 13. The method of claim 12, wherein said eukaryotic cellis a human cell.
 14. The method of claim 2, wherein saidphenotype-converting nucleic acid further comprises one or moreexogenous nucleic acids selected from the group consisting of mRNA,siRNA, miRNA, hnRNA, tRNA, non-coding RNA and combinations thereof. 15.The method of claim 1, wherein said phenotype conversion comprises achange in one or more of gene expression, protein expression,immunological markers, morphology, physiology, synthesis of bioproducts,and membrane lipid composition.
 16. The method of claim 15, whereinphenotype conversion comprises a change in expression of at least 100genes.
 17. The method of claim 15, wherein phenotype conversioncomprises up-regulation of genes associated with chromosomal remodeling.18. The method of claim 15, wherein at least about 5% of differentiallyexpressed genes in said second cell change expression to a levelobserved for said first cell.
 19. The method of claim 1, wherein saidphenotype conversion persists for at least 2 weeks.
 20. The method ofclaim 19, wherein said phenotype conversion persists for the lifetime ofthe cell.
 21. The method of claim 1, wherein the second cell is a haircell that responds to a first range of sound frequencies.
 22. The methodof claim 21, wherein the first cell is a hair cell that responds to asecond range of sound frequencies. 23-26. (canceled)